diff --git a/api/types/kustomization.go b/api/types/kustomization.go
index 878f96658..13b7b9579 100644
--- a/api/types/kustomization.go
+++ b/api/types/kustomization.go
@@ -7,6 +7,7 @@ import (
 	"bytes"
 	"encoding/json"
 	"fmt"
+	"reflect"
 
 	"sigs.k8s.io/kustomize/kyaml/errors"
 	"sigs.k8s.io/kustomize/kyaml/filesys"
@@ -301,21 +302,14 @@ func (k *Kustomization) FixKustomizationPreMarshalling(fSys filesys.FileSystem)
 func (k *Kustomization) CheckEmpty() error {
 	// generate empty Kustomization
 	emptyKustomization := &Kustomization{}
-	emptyKustomization.FixKustomization()
 
-	// compare with yaml string
-	b, err := yaml.Marshal(k)
-	if err != nil {
-		return fmt.Errorf("kustomization marshal error: %w", err)
-	}
-	emptyb, err := yaml.Marshal(emptyKustomization)
-	if err != nil {
-		return fmt.Errorf("empty kustomization marshal error: %w", err)
-	}
+	// k.TypeMeta is metadata. It Isn't related to whether empty or not.
+	emptyKustomization.TypeMeta = k.TypeMeta
 
-	if string(b) == string(emptyb) {
+	if reflect.DeepEqual(k, emptyKustomization) {
 		return fmt.Errorf("kustomization.yaml is empty")
 	}
+
 	return nil
 }
 
diff --git a/api/types/kustomization_test.go b/api/types/kustomization_test.go
index aab4a160e..963f774f6 100644
--- a/api/types/kustomization_test.go
+++ b/api/types/kustomization_test.go
@@ -295,7 +295,7 @@ func TestUnmarshal_Failed(t *testing.T) {
 			kustomizationYamls: []byte(`apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 unknown`),
-			errMsg: "yaml: line 4: could not find expected ':'",
+			errMsg: "invalid Kustomization: yaml: line 4: could not find expected ':'",
 		},
 	}
 	for _, tt := range tests {
@@ -319,6 +319,16 @@ func TestKustomization_CheckEmpty(t *testing.T) {
 			kustomization: &Kustomization{},
 			wantErr:       true,
 		},
+		{
+			name: "empty kustomization.yaml",
+			kustomization: &Kustomization{
+				TypeMeta: TypeMeta{
+					Kind:       KustomizationKind,
+					APIVersion: KustomizationVersion,
+				},
+			},
+			wantErr: true,
+		},
 		{
 			name:          "non empty kustomization.yaml",
 			kustomization: &Kustomization{Resources: []string{"res"}},