diff --git a/web/app/components/evaluation/components/metric-section/__tests__/index.spec.tsx b/web/app/components/evaluation/components/metric-section/__tests__/index.spec.tsx
index 6b240966bf..4cdf58a5dc 100644
--- a/web/app/components/evaluation/components/metric-section/__tests__/index.spec.tsx
+++ b/web/app/components/evaluation/components/metric-section/__tests__/index.spec.tsx
@@ -131,6 +131,23 @@ describe('MetricSection', () => {
       expect(screen.getByText('Answer Node')).toBeInTheDocument()
     })
 
+    it('should remove the builtin metric when removing its last selected node', () => {
+      // Arrange
+      act(() => {
+        useEvaluationStore.getState().addBuiltinMetric(resourceType, resourceId, 'answer-correctness', [
+          { node_id: 'node-answer', title: 'Answer Node', type: 'llm' },
+        ])
+      })
+
+      // Act
+      renderMetricSection()
+      fireEvent.click(screen.getByRole('button', { name: 'Answer Node' }))
+
+      // Assert
+      expect(screen.queryByText('Answer Correctness')).not.toBeInTheDocument()
+      expect(useEvaluationStore.getState().resources[`${resourceType}:${resourceId}`]!.metrics).toHaveLength(0)
+    })
+
     it('should show only unselected nodes in the add-node dropdown and append the selected node', () => {
       // Arrange
       mockUseDefaultEvaluationMetrics.mockReturnValue({
diff --git a/web/app/components/evaluation/components/metric-section/builtin-metric-card.tsx b/web/app/components/evaluation/components/metric-section/builtin-metric-card.tsx
index eb661e3a14..8013ceb2af 100644
--- a/web/app/components/evaluation/components/metric-section/builtin-metric-card.tsx
+++ b/web/app/components/evaluation/components/metric-section/builtin-metric-card.tsx
@@ -39,6 +39,16 @@ const BuiltinMetricCard = ({
     ? availableNodeInfoList.filter(nodeInfo => !selectedNodeIdSet.has(nodeInfo.node_id))
     : []
   const shouldShowAddNode = selectableNodeInfoList.length > 0
+  const handleRemoveNode = (nodeId: string) => {
+    const nextSelectedNodeInfoList = selectedNodeInfoList.filter(item => item.node_id !== nodeId)
+
+    if (nextSelectedNodeInfoList.length === 0) {
+      removeMetric(resourceType, resourceId, metric.id)
+      return
+    }
+
+    updateBuiltinMetric(resourceType, resourceId, metric.optionId, nextSelectedNodeInfoList)
+  }
 
   return (
     <div className="group overflow-hidden rounded-xl border border-components-panel-border hover:bg-background-section">
@@ -92,12 +102,7 @@ const BuiltinMetricCard = ({
                       type="button"
                       className="flex h-4 w-4 items-center justify-center rounded-sm text-text-quaternary transition-colors hover:text-text-secondary"
                       aria-label={nodeInfo.title}
-                      onClick={() => updateBuiltinMetric(
-                        resourceType,
-                        resourceId,
-                        metric.optionId,
-                        selectedNodeInfoList.filter(item => item.node_id !== nodeInfo.node_id),
-                      )}
+                      onClick={() => handleRemoveNode(nodeInfo.node_id)}
                     >
                       <span aria-hidden="true" className="i-custom-vender-solid-general-x-circle h-3.5 w-3.5" />
                     </button>