diff --git a/.github/workflows/ubuntu_test.yaml b/.github/workflows/ubuntu_test.yaml
index aadc775f5..251cf4818 100644
--- a/.github/workflows/ubuntu_test.yaml
+++ b/.github/workflows/ubuntu_test.yaml
@@ -56,7 +56,7 @@ jobs:
         uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: ./kclvm/.kclvm/lcov.info
+          path-to-lcov: ./kclvm/.kclvm_cov/lcov.info
 
       - uses: actions/upload-artifact@v3
         with:
diff --git a/.gitignore b/.gitignore
index 29d5ee571..9595591e4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -77,6 +77,7 @@ lark_parser.pickle
 
 # KCLVM cache and temp output
 .kclvm
+.kclvm_cov
 *.dylib
 *.so
 *.dll
diff --git a/kclvm/cmd/src/test_data/instances/test_inst_11/kcl.mod b/kclvm/cmd/src/test_data/instances/test_inst_11/kcl.mod
new file mode 100644
index 000000000..a626cfb0f
--- /dev/null
+++ b/kclvm/cmd/src/test_data/instances/test_inst_11/kcl.mod
@@ -0,0 +1,5 @@
+[package]
+name = "test_inst_11"
+edition = "0.0.1"
+version = "0.0.1"
+
diff --git a/kclvm/cmd/src/test_data/instances/test_inst_11/model/main.k b/kclvm/cmd/src/test_data/instances/test_inst_11/model/main.k
new file mode 100644
index 000000000..b43778076
--- /dev/null
+++ b/kclvm/cmd/src/test_data/instances/test_inst_11/model/main.k
@@ -0,0 +1,3 @@
+schema K11:
+    msg: str
+    
\ No newline at end of file
diff --git a/kclvm/cmd/src/test_data/instances/test_inst_11/sub/main.k b/kclvm/cmd/src/test_data/instances/test_inst_11/sub/main.k
new file mode 100644
index 000000000..486e93f97
--- /dev/null
+++ b/kclvm/cmd/src/test_data/instances/test_inst_11/sub/main.k
@@ -0,0 +1,5 @@
+import model as m
+
+k11_inst: m.K11 {
+    msg: "k11_in_sub"
+}
\ No newline at end of file
diff --git a/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/expected b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/expected
new file mode 100644
index 000000000..3ad7b524b
--- /dev/null
+++ b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/expected
@@ -0,0 +1,2 @@
+k11_inst:
+  msg: k11_in_main
diff --git a/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/kcl.mod b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/kcl.mod
new file mode 100644
index 000000000..5c0234dc8
--- /dev/null
+++ b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/kcl.mod
@@ -0,0 +1,5 @@
+[package]
+name = "test_inst_111"
+edition = "0.0.1"
+version = "0.0.1"
+
diff --git a/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/kcl.yaml b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/kcl.yaml
new file mode 100644
index 000000000..553e82d00
--- /dev/null
+++ b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/kcl.yaml
@@ -0,0 +1,6 @@
+kcl_cli_configs:
+  file:
+    - ../sub/main.k
+    - ./main.k
+  package_maps:
+    test_inst_11: ./src/test_data/instances/test_inst_11
diff --git a/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/main.k b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/main.k
new file mode 100644
index 000000000..c6985755e
--- /dev/null
+++ b/kclvm/cmd/src/test_data/instances/test_inst_11/test_inst_111/main.k
@@ -0,0 +1,5 @@
+import test_inst_11.model as m
+
+k11_inst: m.K11 {
+    msg= "k11_in_main"
+}
\ No newline at end of file
diff --git a/kclvm/cmd/src/tests.rs b/kclvm/cmd/src/tests.rs
index 9fc2558ca..5d4ba5423 100644
--- a/kclvm/cmd/src/tests.rs
+++ b/kclvm/cmd/src/tests.rs
@@ -472,6 +472,7 @@ fn test_instances_with_yaml() {
         "test_inst_8",
         "test_inst_9",
         "test_inst_10",
+        "test_inst_11/test_inst_111",
     ];
 
     for case in &test_cases {
diff --git a/kclvm/config/src/modfile.rs b/kclvm/config/src/modfile.rs
index 0abe5c010..f5f27b73d 100644
--- a/kclvm/config/src/modfile.rs
+++ b/kclvm/config/src/modfile.rs
@@ -84,7 +84,7 @@ pub struct KCLModFileExpectedSection {
     pub global_version: Option<String>,
 }
 
-pub fn get_pkg_root_from_paths(file_paths: &[String]) -> Result<String, String> {
+pub fn get_pkg_root_from_paths(file_paths: &[String], workdir: String) -> Result<String, String> {
     if file_paths.is_empty() {
         return Err("No input KCL files or paths".to_string());
     }
@@ -107,6 +107,8 @@ pub fn get_pkg_root_from_paths(file_paths: &[String]) -> Result<String, String>
     }
     if m.len() == 1 {
         return Ok(last_root);
+    } else if !workdir.is_empty() {
+        return Ok(workdir);
     }
 
     Err(format!("conflict kcl.mod file paths: {:?}", m))
@@ -162,17 +164,17 @@ mod modfile_test {
     #[test]
     fn test_get_pkg_root_from_paths() {
         assert_eq!(
-            get_pkg_root_from_paths(&[]),
+            get_pkg_root_from_paths(&[], "".to_string()),
             Err("No input KCL files or paths".to_string())
         );
         assert_eq!(
-            get_pkg_root_from_paths(&["wrong_path".to_string()]),
+            get_pkg_root_from_paths(&["wrong_path".to_string()], "".to_string()),
             Ok("".to_string())
         );
         let expected_root = std::path::Path::new(TEST_ROOT).canonicalize().unwrap();
         let expected = expected_root.adjust_canonicalization();
         assert_eq!(
-            get_pkg_root_from_paths(&[SETTINGS_FILE.to_string()]),
+            get_pkg_root_from_paths(&[SETTINGS_FILE.to_string()], "".to_string()),
             Ok(expected.to_string())
         );
     }
diff --git a/kclvm/driver/src/lib.rs b/kclvm/driver/src/lib.rs
index f5314ab2e..6acab4029 100644
--- a/kclvm/driver/src/lib.rs
+++ b/kclvm/driver/src/lib.rs
@@ -77,7 +77,7 @@ pub fn canonicalize_input_files(
     }
 
     // Get the root path of the project
-    let pkgroot = kclvm_config::modfile::get_pkg_root_from_paths(&kcl_paths)?;
+    let pkgroot = kclvm_config::modfile::get_pkg_root_from_paths(&kcl_paths, work_dir)?;
 
     // The second traversal replaces ${KCL_MOD} with the project root path
     kcl_paths = kcl_paths
diff --git a/kclvm/makefile b/kclvm/makefile
index 2e6754e4f..ee29d3e48 100644
--- a/kclvm/makefile
+++ b/kclvm/makefile
@@ -67,8 +67,9 @@ codecov:
 codecov-lcov:
 	rustup component add llvm-tools-preview
 	cargo install cargo-llvm-cov
-	mkdir $(PWD)/.kclvm
-	cargo llvm-cov --lcov --output-path $(PWD)/.kclvm/lcov.info --workspace --ignore-filename-regex gpyrpc.rs -- --nocapture
+	rm -rf $(PWD)/.kclvm_cov
+	mkdir $(PWD)/.kclvm_cov
+	cargo llvm-cov --lcov --output-path $(PWD)/.kclvm_cov/lcov.info --workspace --ignore-filename-regex gpyrpc.rs -- --nocapture
 
 # Test runtime libaries using python functions
 test-runtime: install-kclvm-py install-pytest
diff --git a/kclvm/parser/src/entry.rs b/kclvm/parser/src/entry.rs
index 71c2bd980..a49f3d415 100644
--- a/kclvm/parser/src/entry.rs
+++ b/kclvm/parser/src/entry.rs
@@ -15,6 +15,7 @@ use crate::LoadProgramOptions;
 /// The reason why the [`Entries`] is not an [`IndexMap`] is that the [`entries`] is duplicable and ordered.
 #[derive(Default, Debug)]
 pub struct Entries {
+    root_path: String,
     entries: VecDeque<Entry>,
 }
 
@@ -109,6 +110,11 @@ impl Entries {
         self.entries.iter_mut().try_for_each(f)?;
         return Ok(());
     }
+
+    /// [`get_root_path`] will return the root path of [`Entries`].
+    pub fn get_root_path(&self) -> &String {
+        &self.root_path
+    }
 }
 
 /// [`Entry`] is a package name and package root path pair.
@@ -345,50 +351,54 @@ pub fn get_compile_entries_from_paths(
         result.push_entry(entry);
     }
 
-    // The main 'kcl.mod' path can be found only once.
-    // Replace all the '${KCL_MOD}' with the real path of main 'kcl.mod'.
-    if result
+    let pkg_root = if result
         .get_unique_normal_paths_by_name(kclvm_ast::MAIN_PKG)
         .len()
         == 1
+        && opts.work_dir.is_empty()
     {
-        // If the [`ModRelativePath`] with preffix '${KCL_MOD}'.
-        // Replace the '${KCL_MOD}' by the root path of package '__main__'.
-
-        // Calculate the root path of package '__main__'.
-        let pkg_root;
-        let main_entry = result
-            .get_nth_entry_by_name(0, kclvm_ast::MAIN_PKG)
-            .ok_or_else(|| format!("program entry not found in {:?}", file_paths))?;
-        pkg_root = main_entry.path().to_string();
-
-        // Replace the '${KCL_MOD}' of all the paths with package name '__main__'.
-        result.apply_to_all_entries(|entry| {
-            let path = ModRelativePath::from(entry.path().to_string());
-            if entry.name() == kclvm_ast::MAIN_PKG
-                && path.is_relative_path().map_err(|err| err.to_string())?
-            {
-                entry.set_path(pkg_root.to_string());
-                entry.extend_k_files(get_main_files_from_pkg_path(
-                    &path
-                        .canonicalize_by_root_path(&pkg_root)
-                        .map_err(|err| err.to_string())?,
-                    &pkg_root,
-                    &kclvm_ast::MAIN_PKG.to_string(),
-                    opts,
-                )?);
-            }
-            return Ok(());
-        })?;
-        return Ok(result);
-    }
+        // If the 'kcl.mod' can be found only once, the package root path will be the path of the 'kcl.mod'.
+        result
+            .get_unique_normal_paths_by_name(kclvm_ast::MAIN_PKG)
+            .get(0)
+            .unwrap()
+            .to_string()
+    } else if !opts.work_dir.is_empty() {
+        // If the 'kcl.mod' can be found more than once, the package root path will be the 'work_dir'.
+        if let Some(root_work_dir) = get_pkg_root(&opts.work_dir) {
+            root_work_dir
+        } else {
+            "".to_string()
+        }
+    } else {
+        // If there are more than one main 'kcl.mod' files, return error.
+        // the root path of package '__main__' can only one.
+        return Err(format!(
+            "conflict kcl.mod file paths: {:?}",
+            result.get_unique_normal_paths_by_name(kclvm_ast::MAIN_PKG)
+        ));
+    };
+    result.root_path = pkg_root.clone();
+    // Replace the '${KCL_MOD}' of all the paths with package name '__main__'.
+    result.apply_to_all_entries(|entry| {
+        let path = ModRelativePath::from(entry.path().to_string());
+        if entry.name() == kclvm_ast::MAIN_PKG
+            && path.is_relative_path().map_err(|err| err.to_string())?
+        {
+            entry.set_path(pkg_root.to_string());
+            entry.extend_k_files(get_main_files_from_pkg_path(
+                &path
+                    .canonicalize_by_root_path(&pkg_root)
+                    .map_err(|err| err.to_string())?,
+                &pkg_root,
+                &kclvm_ast::MAIN_PKG.to_string(),
+                opts,
+            )?);
+        }
+        return Ok(());
+    })?;
 
-    // If there are more than one main 'kcl.mod' files, return error.
-    // the root path of package '__main__' can only one.
-    Err(format!(
-        "conflict kcl.mod file paths: {:?}",
-        result.get_unique_normal_paths_by_name(kclvm_ast::MAIN_PKG)
-    ))
+    return Ok(result);
 }
 
 /// Get files in the main package with the package root.
diff --git a/kclvm/parser/src/lib.rs b/kclvm/parser/src/lib.rs
index 70c7d1d50..0cd42ecb8 100644
--- a/kclvm/parser/src/lib.rs
+++ b/kclvm/parser/src/lib.rs
@@ -313,10 +313,7 @@ impl Loader {
     fn _load_main(&mut self) -> Result<ast::Program, String> {
         let compile_entries = get_compile_entries_from_paths(&self.paths, &self.opts)?;
         let mut pkgs = HashMap::new();
-
-        let main_program_root = compile_entries
-            .contains_pkg_name(&kclvm_ast::MAIN_PKG.to_string())
-            .ok_or(format!("main package not found in {:?}", &self.paths))?;
+        let workdir = compile_entries.get_root_path().to_string();
 
         debug_assert_eq!(compile_entries.len(), self.paths.len());
 
@@ -349,7 +346,7 @@ impl Loader {
         // Insert the complete ast to replace the empty list.
         pkgs.insert(kclvm_ast::MAIN_PKG.to_string(), pkg_files);
         Ok(ast::Program {
-            root: main_program_root.path().to_string(),
+            root: workdir,
             main: kclvm_ast::MAIN_PKG.to_string(),
             pkgs,
         })
diff --git a/kclvm/tools/src/LSP/src/request.rs b/kclvm/tools/src/LSP/src/request.rs
index 68319eb3b..f1a12d03a 100644
--- a/kclvm/tools/src/LSP/src/request.rs
+++ b/kclvm/tools/src/LSP/src/request.rs
@@ -1,5 +1,5 @@
+use anyhow::Ok;
 use crossbeam_channel::Sender;
-
 use lsp_types::TextEdit;
 use ra_ap_vfs::VfsPath;
 use std::time::Instant;