diff --git a/flink-cdc-runtime/src/main/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransform.java b/flink-cdc-runtime/src/main/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransform.java
index 742322d7826..03128aeef75 100644
--- a/flink-cdc-runtime/src/main/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransform.java
+++ b/flink-cdc-runtime/src/main/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransform.java
@@ -50,14 +50,14 @@ public SchemaMetadataTransform(
         if (!StringUtils.isNullOrWhitespaceOnly(primaryKeyString)) {
             String[] primaryKeyArr = primaryKeyString.split(",");
             for (int i = 0; i < primaryKeyArr.length; i++) {
-                primaryKeyArr[i] = primaryKeyArr[i].trim();
+                primaryKeyArr[i] = normalizeColumnReference(primaryKeyArr[i]);
             }
             primaryKeys = Arrays.asList(primaryKeyArr);
         }
         if (!StringUtils.isNullOrWhitespaceOnly(partitionKeyString)) {
             String[] partitionKeyArr = partitionKeyString.split(",");
             for (int i = 0; i < partitionKeyArr.length; i++) {
-                partitionKeyArr[i] = partitionKeyArr[i].trim();
+                partitionKeyArr[i] = normalizeColumnReference(partitionKeyArr[i]);
             }
             partitionKeys = Arrays.asList(partitionKeyArr);
         }
@@ -86,6 +86,14 @@ public SchemaMetadataTransform(
         }
     }
 
+    private String normalizeColumnReference(String columnReference) {
+        String trimmed = columnReference.trim();
+        if (trimmed.length() >= 2 && trimmed.startsWith("`") && trimmed.endsWith("`")) {
+            return trimmed.substring(1, trimmed.length() - 1).replace("``", "`");
+        }
+        return trimmed;
+    }
+
     public List<String> getPrimaryKeys() {
         return primaryKeys;
     }
diff --git a/flink-cdc-runtime/src/test/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransformTest.java b/flink-cdc-runtime/src/test/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransformTest.java
index d12f669fe0b..49b65df07f2 100644
--- a/flink-cdc-runtime/src/test/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransformTest.java
+++ b/flink-cdc-runtime/src/test/java/org/apache/flink/cdc/runtime/operators/transform/SchemaMetadataTransformTest.java
@@ -24,6 +24,16 @@
 /** Testcases for {@link SchemaMetadataTransform}. */
 class SchemaMetadataTransformTest {
 
+    @Test
+    void testPrimaryAndPartitionKeysStripBackticks() {
+        SchemaMetadataTransform transform =
+                new SchemaMetadataTransform(
+                        "id, `order-id`, `customer``name`", "region, `order-id`", null, null);
+
+        assertThat(transform.getPrimaryKeys()).containsExactly("id", "order-id", "customer`name");
+        assertThat(transform.getPartitionKeys()).containsExactly("region", "order-id");
+    }
+
     @Test
     void testTableOptionsWithCommaDelimiter() {
         SchemaMetadataTransform transform =