diff --git a/pkg/controllers/subnetset/subnetset_controller.go b/pkg/controllers/subnetset/subnetset_controller.go
index 6a4aefc50..5c06f48e3 100644
--- a/pkg/controllers/subnetset/subnetset_controller.go
+++ b/pkg/controllers/subnetset/subnetset_controller.go
@@ -262,7 +262,7 @@ func (r *SubnetSetReconciler) CollectGarbage(ctx context.Context) {
 		log.Info("SubnetSet garbage collection completed", "duration(ms)", time.Since(startTime).Milliseconds())
 	}()
 
-	crdSubnetSetIDs, err := r.listSubnetSetIDsFromCRs(ctx)
+	crdSubnetSetIDs, err := r.listSubnetSetIDsFromCRs(ctx, true)
 	if err != nil {
 		log.Error(err, "Failed to list Subnet CRs")
 		return
@@ -306,7 +306,7 @@ func (r *SubnetSetReconciler) deleteSubnetForSubnetSet(obj v1alpha1.SubnetSet, u
 	return nil
 }
 
-func (r *SubnetSetReconciler) listSubnetSetIDsFromCRs(ctx context.Context) ([]string, error) {
+func (r *SubnetSetReconciler) listSubnetSetIDsFromCRs(ctx context.Context, deleteSubnetForSubnetSet bool) ([]string, error) {
 	crdSubnetSetList := &v1alpha1.SubnetSetList{}
 	err := r.Client.List(ctx, crdSubnetSetList)
 	if err != nil {
@@ -317,6 +317,15 @@ func (r *SubnetSetReconciler) listSubnetSetIDsFromCRs(ctx context.Context) ([]st
 	for _, sr := range crdSubnetSetList.Items {
 		crdSubnetSetIDs = append(crdSubnetSetIDs, string(sr.UID))
 	}
+	if deleteSubnetForSubnetSet {
+		for _, subnetSet := range crdSubnetSetList.Items {
+			if err := r.deleteSubnetForSubnetSet(subnetSet, true); err != nil {
+				metrics.CounterInc(r.SubnetService.NSXConfig, metrics.ControllerDeleteFailTotal, MetricResTypeSubnetSet)
+			} else {
+				metrics.CounterInc(r.SubnetService.NSXConfig, metrics.ControllerDeleteSuccessTotal, MetricResTypeSubnetSet)
+			}
+		}
+	}
 	return crdSubnetSetIDs, nil
 }
 
@@ -339,7 +348,7 @@ func (r *SubnetSetReconciler) deleteSubnets(nsxSubnets []*model.VpcSubnet) error
 }
 
 func (r *SubnetSetReconciler) deleteStaleSubnets(ctx context.Context, nsxSubnets []*model.VpcSubnet) error {
-	crdSubnetSetIDs, err := r.listSubnetSetIDsFromCRs(ctx)
+	crdSubnetSetIDs, err := r.listSubnetSetIDsFromCRs(ctx, false)
 	if err != nil {
 		log.Error(err, "Failed to list Subnet CRs")
 		return err