diff --git a/hack/testdata/pod-run-as-non-root.yaml b/hack/testdata/pod-run-as-non-root.yaml
new file mode 100644
index 00000000000..330088260b3
--- /dev/null
+++ b/hack/testdata/pod-run-as-non-root.yaml
@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  labels:
+    run: target
+  name: target
+spec:
+  securityContext:
+    runAsUser: 1000
+    runAsGroup: 1000
+    runAsNonRoot: true
+  containers:
+  - image: busybox
+    name: target
+    command: ["/bin/sh", "-c", "sleep 100"]
diff --git a/staging/src/k8s.io/kubectl/pkg/cmd/debug/debug.go b/staging/src/k8s.io/kubectl/pkg/cmd/debug/debug.go
index 1cb325be988..8df40aefa92 100644
--- a/staging/src/k8s.io/kubectl/pkg/cmd/debug/debug.go
+++ b/staging/src/k8s.io/kubectl/pkg/cmd/debug/debug.go
@@ -75,6 +75,9 @@ var (
 		            debugging utilities without restarting the pod.
 		* Node: Create a new pod that runs in the node's host namespaces and can access
 		        the node's filesystem.
+
+		Note: When a non-root user is configured for the entire target Pod, some capabilities granted 
+		by debug profile may not work.
 `))
 
 	debugExample = templates.Examples(i18n.T(`
@@ -495,6 +498,8 @@ func (o *DebugOptions) debugByEphemeralContainer(ctx context.Context, pod *corev
 	}
 	klog.V(2).Infof("new ephemeral container: %#v", debugContainer)
 
+	o.displayWarning((*corev1.Container)(&debugContainer.EphemeralContainerCommon), pod)
+
 	debugJS, err := json.Marshal(debugPod)
 	if err != nil {
 		return nil, "", fmt.Errorf("error creating JSON for debug container: %v", err)
@@ -611,6 +616,16 @@ func (o *DebugOptions) debugByCopy(ctx context.Context, pod *corev1.Pod) (*corev
 	if err != nil {
 		return nil, "", err
 	}
+
+	var debugContainer *corev1.Container
+	for i := range copied.Spec.Containers {
+		if copied.Spec.Containers[i].Name == dc {
+			debugContainer = &copied.Spec.Containers[i]
+			break
+		}
+	}
+	o.displayWarning(debugContainer, copied)
+
 	created, err := o.podClient.Pods(copied.Namespace).Create(ctx, copied, metav1.CreateOptions{})
 	if err != nil {
 		return nil, "", err
@@ -624,6 +639,32 @@ func (o *DebugOptions) debugByCopy(ctx context.Context, pod *corev1.Pod) (*corev
 	return created, dc, nil
 }
 
+// Display warning message if some capabilities are set by profile and non-root user is specified in .Spec.SecurityContext.RunAsUser.(#1650)
+func (o *DebugOptions) displayWarning(container *corev1.Container, pod *corev1.Pod) {
+	if container == nil {
+		return
+	}
+
+	if pod.Spec.SecurityContext.RunAsUser == nil || *pod.Spec.SecurityContext.RunAsUser == 0 {
+		return
+	}
+
+	if container.SecurityContext == nil {
+		return
+	}
+
+	if container.SecurityContext.RunAsUser != nil && *container.SecurityContext.RunAsUser == 0 {
+		return
+	}
+
+	if (container.SecurityContext.Privileged == nil || !*container.SecurityContext.Privileged) &&
+		(container.SecurityContext.Capabilities == nil || len(container.SecurityContext.Capabilities.Add) == 0) {
+		return
+	}
+
+	_, _ = fmt.Fprintln(o.ErrOut, `Warning: Non-root user is configured for the entire target Pod, and some capabilities granted by debug profile may not work. Please consider using "--custom" with a custom profile that specifies "securityContext.runAsUser: 0".`)
+}
+
 // generateDebugContainer returns a debugging pod and an EphemeralContainer suitable for use as a debug container
 // in the given pod.
 func (o *DebugOptions) generateDebugContainer(pod *corev1.Pod) (*corev1.Pod, *corev1.EphemeralContainer, error) {
diff --git a/test/cmd/debug.sh b/test/cmd/debug.sh
index bb49fa2d1fc..f8b4e53e211 100755
--- a/test/cmd/debug.sh
+++ b/test/cmd/debug.sh
@@ -659,3 +659,34 @@ EOF
   set +o nounset
   set +o errexit
 }
+
+run_kubectl_debug_warning_tests() {
+  set -o nounset
+  set -o errexit
+
+  create_and_use_new_namespace  
+  kube::log::status "Testing kubectl debug warning"
+
+  ### Non-root Pod Troubleshooting by ephemeral containers
+  # Pre-Condition: Non-root Pod "busybox" is created 
+  kubectl create -f hack/testdata/pod-run-as-non-root.yaml  "${kube_flags[@]:?}"
+  kube::test::get_object_assert pod "{{range.items}}{{${id_field:?}}}:{{end}}" 'target:'
+  # Command: add a new debug container with netadmin profile
+  output_message=$(kubectl debug target -it --image=busybox --container=debug-container --attach=false --profile=netadmin "${kube_flags[@]:?}" 2>&1)
+  kube::test::if_has_string "${output_message}" 'Warning: Non-root user is configured for the entire target Pod, and some capabilities granted by debug profile may not work. Please consider using "--custom" with a custom profile that specifies "securityContext.runAsUser: 0".'
+  # Clean up
+  kubectl delete pod target "${kube_flags[@]:?}"
+
+  ### Non-root Pod Troubleshooting by pod copy
+  # Pre-Condition: Non-root Pod "busybox" is created 
+  kubectl create -f hack/testdata/pod-run-as-non-root.yaml  "${kube_flags[@]:?}"
+  kube::test::get_object_assert pod "{{range.items}}{{${id_field:?}}}:{{end}}" 'target:'
+  # Command: create a copy of target with a new debug container
+  output_message=$(kubectl debug target -it --copy-to=target-copy --image=busybox --container=debug-container --attach=false --profile=netadmin "${kube_flags[@]:?}" 2>&1)
+  kube::test::if_has_string "${output_message}" 'Warning: Non-root user is configured for the entire target Pod, and some capabilities granted by debug profile may not work. Please consider using "--custom" with a custom profile that specifies "securityContext.runAsUser: 0".'
+  # Clean up
+  kubectl delete pod target "${kube_flags[@]:?}"
+
+  set +o nounset
+  set +o errexit
+}
diff --git a/test/cmd/legacy-script.sh b/test/cmd/legacy-script.sh
index 4f9177a5612..ebcefb676f1 100755
--- a/test/cmd/legacy-script.sh
+++ b/test/cmd/legacy-script.sh
@@ -1048,6 +1048,7 @@ runTests() {
     record_command run_kubectl_debug_restricted_tests
     record_command run_kubectl_debug_netadmin_tests
     record_command run_kubectl_debug_custom_profile_tests
+    record_command run_kubectl_debug_warning_tests
   fi
   if kube::test::if_supports_resource "${nodes}" ; then
     record_command run_kubectl_debug_node_tests