diff --git a/pkg/detector/detector.go b/pkg/detector/detector.go
index 1ec920ccf..94ad42355 100644
--- a/pkg/detector/detector.go
+++ b/pkg/detector/detector.go
@@ -479,7 +479,7 @@ func (d *ResourceDetector) ApplyClusterPolicy(object *unstructured.Unstructured,
 						"try again later after binding is garbage collected, see https://github.com/karmada-io/karmada/issues/2090")
 				}
 				// Just update necessary fields, especially avoid modifying Spec.Clusters which is scheduling result, if already exists.
-				bindingCopy.Labels = binding.Labels
+				bindingCopy.Labels = util.DedupeAndMergeLabels(bindingCopy.Labels, binding.Labels)
 				bindingCopy.OwnerReferences = binding.OwnerReferences
 				bindingCopy.Finalizers = binding.Finalizers
 				bindingCopy.Spec.Resource = binding.Spec.Resource
@@ -523,7 +523,7 @@ func (d *ResourceDetector) ApplyClusterPolicy(object *unstructured.Unstructured,
 					"try again later after binding is garbage collected, see https://github.com/karmada-io/karmada/issues/2090")
 			}
 			// Just update necessary fields, especially avoid modifying Spec.Clusters which is scheduling result, if already exists.
-			bindingCopy.Labels = binding.Labels
+			bindingCopy.Labels = util.DedupeAndMergeLabels(bindingCopy.Labels, binding.Labels)
 			bindingCopy.OwnerReferences = binding.OwnerReferences
 			bindingCopy.Finalizers = binding.Finalizers
 			bindingCopy.Spec.Resource = binding.Spec.Resource