diff --git a/multicluster/controllers/multicluster/stale_controller.go b/multicluster/controllers/multicluster/stale_controller.go
index 5c1b031d48a..a84bfbc2abf 100644
--- a/multicluster/controllers/multicluster/stale_controller.go
+++ b/multicluster/controllers/multicluster/stale_controller.go
@@ -339,7 +339,7 @@ func (c *StaleResCleanupController) cleanupLabelIdentityResourceExport(commonAre
 		if !ok {
 			continue
 		}
-		normalizedLabel := podNSlabel + "&pod:" + labels.FormatLabels(p.Labels)
+		normalizedLabel := podNSlabel + "&pod:" + labels.Set(p.Labels).String()
 		delete(staleResExpItems, normalizedLabel)
 	}
 	for _, r := range staleResExpItems {
diff --git a/multicluster/controllers/multicluster/stale_controller_test.go b/multicluster/controllers/multicluster/stale_controller_test.go
index 97949ebd5ca..a3f7a47738a 100644
--- a/multicluster/controllers/multicluster/stale_controller_test.go
+++ b/multicluster/controllers/multicluster/stale_controller_test.go
@@ -312,10 +312,18 @@ func TestStaleController_CleanupResourceExport(t *testing.T) {
 					},
 				},
 			},
+			{
+				ObjectMeta: metav1.ObjectMeta{
+					Namespace: "test-ns",
+					Name:      "test-pod-empty-labels",
+				},
+			},
 		},
 	}
 	labelNormalizedExist := "ns:kubernetes.io/metadata.name=test-ns,purpose=test&pod:app=web"
 	labelNormalizedNonExist := "ns:kubernetes.io/metadata.name=test-ns,purpose=test&pod:app=db"
+	labelNormalizedEmptyLabels := "ns:kubernetes.io/metadata.name=test-ns,purpose=test&pod:"
+	labelNormalizedEmptyLabelsStale := "ns:kubernetes.io/metadata.name=test-ns,purpose=test&pod:<none>"
 	toKeepLabelResExport := mcsv1alpha1.ResourceExport{
 		ObjectMeta: metav1.ObjectMeta{
 			Namespace: "default",
@@ -332,6 +340,22 @@ func TestStaleController_CleanupResourceExport(t *testing.T) {
 			},
 		},
 	}
+	toKeepLabelResExportEmptyLabels := mcsv1alpha1.ResourceExport{
+		ObjectMeta: metav1.ObjectMeta{
+			Namespace: "default",
+			Name:      "cluster-a-" + common.HashLabelIdentity(labelNormalizedEmptyLabels),
+			Labels: map[string]string{
+				constants.SourceKind:      constants.LabelIdentityKind,
+				constants.SourceClusterID: "cluster-a",
+			},
+		},
+		Spec: mcsv1alpha1.ResourceExportSpec{
+			Kind: constants.LabelIdentityKind,
+			LabelIdentity: &mcsv1alpha1.LabelIdentityExport{
+				NormalizedLabel: labelNormalizedEmptyLabels,
+			},
+		},
+	}
 	toDeleteLabelResExport := mcsv1alpha1.ResourceExport{
 		ObjectMeta: metav1.ObjectMeta{
 			Namespace: "default",
@@ -348,6 +372,22 @@ func TestStaleController_CleanupResourceExport(t *testing.T) {
 			},
 		},
 	}
+	toDeleteLabelResExportEmptyLabels := mcsv1alpha1.ResourceExport{
+		ObjectMeta: metav1.ObjectMeta{
+			Namespace: "default",
+			Name:      "cluster-a-" + common.HashLabelIdentity(labelNormalizedEmptyLabelsStale),
+			Labels: map[string]string{
+				constants.SourceKind:      constants.LabelIdentityKind,
+				constants.SourceClusterID: "cluster-a",
+			},
+		},
+		Spec: mcsv1alpha1.ResourceExportSpec{
+			Kind: constants.LabelIdentityKind,
+			LabelIdentity: &mcsv1alpha1.LabelIdentityExport{
+				NormalizedLabel: labelNormalizedEmptyLabelsStale,
+			},
+		},
+	}
 	tests := []struct {
 		name                   string
 		existSvcList           *corev1.ServiceList
@@ -375,6 +415,8 @@ func TestStaleController_CleanupResourceExport(t *testing.T) {
 					toKeepSvcResExport,
 					toKeepLabelResExport,
 					toDeleteLabelResExport,
+					toKeepLabelResExportEmptyLabels,
+					toDeleteLabelResExportEmptyLabels,
 					svcResExportFromOtherCluster,
 				},
 			},
@@ -396,8 +438,8 @@ func TestStaleController_CleanupResourceExport(t *testing.T) {
 			err := fakeRemoteClient.List(context.TODO(), resExpList, &client.ListOptions{})
 			resExpLen := len(resExpList.Items)
 			if err == nil {
-				if resExpLen != 3 {
-					t.Errorf("Should only THREE valid ResourceExports left but got %v", resExpLen)
+				if resExpLen != 4 {
+					t.Errorf("Should only FOUR valid ResourceExports left but got %v", resExpLen)
 				}
 			} else {
 				t.Errorf("Should list ResourceExport successfully but got err = %v", err)
diff --git a/pkg/controller/labelidentity/label_group_index.go b/pkg/controller/labelidentity/label_group_index.go
index 79d3d4d633a..7de65a845ea 100644
--- a/pkg/controller/labelidentity/label_group_index.go
+++ b/pkg/controller/labelidentity/label_group_index.go
@@ -124,7 +124,12 @@ func (l *labelIdentityMatch) matches(s *selectorItem) bool {
 // constructMapFromLabelString parses label string of format "app=client,env=dev" into a map.
 func constructMapFromLabelString(s string) map[string]string {
 	m := map[string]string{}
-	if s == "" {
+	// Before https://github.com/antrea-io/antrea/issues/5403 is fixed, LabelIdentities created
+	// for Pods with an empty label set will include a <none> string. Handling for such LabelIdentities
+	// are needed, as in multi-cluster controller upgrade cases, these LabelIdentities created by
+	// previous controller still need to be processed, but will be cleaned up by the stale controller
+	// eventually.
+	if s == "" || s == "<none>" {
 		return m
 	}
 	kvs := strings.Split(s, ",")
diff --git a/pkg/controller/labelidentity/label_group_index_test.go b/pkg/controller/labelidentity/label_group_index_test.go
index 651118a2fef..b710d95c8aa 100644
--- a/pkg/controller/labelidentity/label_group_index_test.go
+++ b/pkg/controller/labelidentity/label_group_index_test.go
@@ -65,10 +65,11 @@ var (
 	selectorItemG = &selectorItem{
 		selector: selectorG,
 	}
-	labelA = "ns:kubernetes.io/metadata.name=testing,purpose=test&pod:app=web"
-	labelB = "ns:kubernetes.io/metadata.name=testing,purpose=test&pod:app=db"
-	labelC = "ns:kubernetes.io/metadata.name=nomatch,purpose=nomatch&pod:app=db"
-	labelD = "ns:kubernetes.io/metadata.name=testing,purpose=test&pod:"
+	labelA     = "ns:kubernetes.io/metadata.name=testing,purpose=test&pod:app=web"
+	labelB     = "ns:kubernetes.io/metadata.name=testing,purpose=test&pod:app=db"
+	labelC     = "ns:kubernetes.io/metadata.name=nomatch,purpose=nomatch&pod:app=db"
+	labelD     = "ns:kubernetes.io/metadata.name=testing,purpose=test&pod:"
+	labelStale = "ns:kubernetes.io/metadata.name=testing,purpose=test&pod:<none>"
 )
 
 func TestLabelIdentityMatch(t *testing.T) {
@@ -172,6 +173,11 @@ func TestLabelIdentityMatch(t *testing.T) {
 			selector:    selectorItemG,
 			expectMatch: true,
 		},
+		{
+			label:       labelStale,
+			selector:    selectorItemA,
+			expectMatch: false,
+		},
 	}
 	for _, tt := range tests {
 		labelMatch := newLabelIdentityMatch(tt.label, 1)