diff --git a/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/CustomAggExpressionTransformer.scala b/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/CustomAggExpressionTransformer.scala
index 757795bf8634..43decfba28b7 100644
--- a/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/CustomAggExpressionTransformer.scala
+++ b/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/CustomAggExpressionTransformer.scala
@@ -19,8 +19,11 @@ package io.glutenproject.execution.extension
 import io.glutenproject.expression._
 import io.glutenproject.extension.ExpressionExtensionTrait
 
+import org.apache.spark.sql.catalyst.expressions._
 import org.apache.spark.sql.catalyst.expressions.aggregate._
 
+import scala.collection.mutable.ListBuffer
+
 case class CustomAggExpressionTransformer() extends ExpressionExtensionTrait {
 
   lazy val expressionSigs = Seq(
@@ -29,4 +32,33 @@ case class CustomAggExpressionTransformer() extends ExpressionExtensionTrait {
 
   /** Generate the extension expressions list, format: Sig[XXXExpression]("XXXExpressionName") */
   override def expressionSigList: Seq[Sig] = expressionSigs
+
+  /** Get the attribute index of the extension aggregate functions. */
+  override def getAttrsIndexForExtensionAggregateExpr(
+      aggregateFunc: AggregateFunction,
+      mode: AggregateMode,
+      exp: AggregateExpression,
+      aggregateAttributeList: Seq[Attribute],
+      aggregateAttr: ListBuffer[Attribute],
+      resIndex: Int): Int = {
+    var reIndex = resIndex
+    aggregateFunc match {
+      case CustomSum(_, _) =>
+        mode match {
+          case Partial =>
+            val aggBufferAttr = aggregateFunc.inputAggBufferAttributes
+            val attr = ConverterUtils.getAttrFromExpr(aggBufferAttr.head)
+            aggregateAttr += attr
+            reIndex += 1
+            reIndex
+          // custom logic: can not support 'Final'
+          /* case Final =>
+            aggregateAttr += aggregateAttributeList(reIndex)
+            reIndex += 1
+            reIndex */
+          case other =>
+            throw new UnsupportedOperationException(s"Unsupported aggregate mode: $other.")
+        }
+    }
+  }
 }
diff --git a/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/GlutenCustomAggExpressionSuite.scala b/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/GlutenCustomAggExpressionSuite.scala
index 25a7c7d012ab..3a52e0e7b148 100644
--- a/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/GlutenCustomAggExpressionSuite.scala
+++ b/backends-clickhouse/src/test/scala/io/glutenproject/execution/extension/GlutenCustomAggExpressionSuite.scala
@@ -16,17 +16,15 @@
  */
 package io.glutenproject.execution.extension
 
-import io.glutenproject.execution.{GlutenClickHouseTPCHAbstractSuite, HashAggregateExecBaseTransformer}
+import io.glutenproject.execution.{GlutenClickHouseTPCHAbstractSuite, WholeStageTransformerSuite}
 
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.catalyst.FunctionIdentifier
 import org.apache.spark.sql.catalyst.analysis.FunctionRegistryBase
 import org.apache.spark.sql.catalyst.expressions.aggregate.CustomSum
-import org.apache.spark.sql.execution.adaptive.AdaptiveSparkPlanHelper
+import org.apache.spark.sql.execution.aggregate.HashAggregateExec
 
-class GlutenCustomAggExpressionSuite
-  extends GlutenClickHouseTPCHAbstractSuite
-  with AdaptiveSparkPlanHelper {
+class GlutenCustomAggExpressionSuite extends GlutenClickHouseTPCHAbstractSuite {
 
   override protected val resourcePath: String =
     "../../../../gluten-core/src/test/resources/tpch-data"
@@ -77,19 +75,13 @@ class GlutenCustomAggExpressionSuite
          |    l_returnflag,
          |    l_linestatus;
          |""".stripMargin
-    compareResultsAgainstVanillaSpark(
-      sql,
-      true,
-      {
-        df =>
-          val hashAggExec = collect(df.queryExecution.executedPlan) {
-            case hash: HashAggregateExecBaseTransformer => hash
-          }
-          assert(hashAggExec.size == 2)
+    val df = spark.sql(sql)
+    // Final stage is not supported, it will be fallback
+    WholeStageTransformerSuite.checkFallBack(df, false)
 
-          assert(hashAggExec(0).aggregateExpressions(0).aggregateFunction.isInstanceOf[CustomSum])
-          assert(hashAggExec(1).aggregateExpressions(0).aggregateFunction.isInstanceOf[CustomSum])
-      }
-    )
+    val fallbackAggExec = df.queryExecution.executedPlan.collect {
+      case agg: HashAggregateExec => agg
+    }
+    assert(fallbackAggExec.size == 1)
   }
 }
diff --git a/gluten-core/src/main/scala/io/glutenproject/execution/HashAggregateExecBaseTransformer.scala b/gluten-core/src/main/scala/io/glutenproject/execution/HashAggregateExecBaseTransformer.scala
index e88b87e7a4a0..25298c53f710 100644
--- a/gluten-core/src/main/scala/io/glutenproject/execution/HashAggregateExecBaseTransformer.scala
+++ b/gluten-core/src/main/scala/io/glutenproject/execution/HashAggregateExecBaseTransformer.scala
@@ -408,25 +408,40 @@ abstract class HashAggregateExecBaseTransformer(
     var resIndex = index
     val mode = exp.mode
     val aggregateFunc = exp.aggregateFunction
-    if (!checkAggFuncModeSupport(aggregateFunc, mode)) {
-      throw new UnsupportedOperationException(
-        s"Unsupported aggregate mode: $mode for ${aggregateFunc.prettyName}")
-    }
-    mode match {
-      case Partial | PartialMerge =>
-        val aggBufferAttr = aggregateFunc.inputAggBufferAttributes
-        for (index <- aggBufferAttr.indices) {
-          val attr = ConverterUtils.getAttrFromExpr(aggBufferAttr(index))
-          aggregateAttr += attr
-        }
-        resIndex += aggBufferAttr.size
-        resIndex
-      case Final =>
-        aggregateAttr += aggregateAttributeList(resIndex)
-        resIndex += 1
-        resIndex
-      case other =>
-        throw new UnsupportedOperationException(s"Unsupported aggregate mode: $other.")
+    // First handle the custom aggregate functions
+    if (
+      ExpressionMappings.expressionExtensionTransformer.extensionExpressionsMapping.contains(
+        aggregateFunc.getClass)
+    ) {
+      ExpressionMappings.expressionExtensionTransformer
+        .getAttrsIndexForExtensionAggregateExpr(
+          aggregateFunc,
+          mode,
+          exp,
+          aggregateAttributeList,
+          aggregateAttr,
+          index)
+    } else {
+      if (!checkAggFuncModeSupport(aggregateFunc, mode)) {
+        throw new UnsupportedOperationException(
+          s"Unsupported aggregate mode: $mode for ${aggregateFunc.prettyName}")
+      }
+      mode match {
+        case Partial | PartialMerge =>
+          val aggBufferAttr = aggregateFunc.inputAggBufferAttributes
+          for (index <- aggBufferAttr.indices) {
+            val attr = ConverterUtils.getAttrFromExpr(aggBufferAttr(index))
+            aggregateAttr += attr
+          }
+          resIndex += aggBufferAttr.size
+          resIndex
+        case Final =>
+          aggregateAttr += aggregateAttributeList(resIndex)
+          resIndex += 1
+          resIndex
+        case other =>
+          throw new UnsupportedOperationException(s"Unsupported aggregate mode: $other.")
+      }
     }
   }
 
diff --git a/gluten-core/src/main/scala/io/glutenproject/extension/ExpressionExtensionTrait.scala b/gluten-core/src/main/scala/io/glutenproject/extension/ExpressionExtensionTrait.scala
index 5a5fb08c3c91..d1fc219b7bbb 100644
--- a/gluten-core/src/main/scala/io/glutenproject/extension/ExpressionExtensionTrait.scala
+++ b/gluten-core/src/main/scala/io/glutenproject/extension/ExpressionExtensionTrait.scala
@@ -20,6 +20,9 @@ import io.glutenproject.expression.{ExpressionTransformer, Sig}
 
 import org.apache.spark.internal.Logging
 import org.apache.spark.sql.catalyst.expressions.{Attribute, Expression}
+import org.apache.spark.sql.catalyst.expressions.aggregate.{AggregateExpression, AggregateFunction, AggregateMode}
+
+import scala.collection.mutable.ListBuffer
 
 trait ExpressionExtensionTrait {
 
@@ -37,6 +40,18 @@ trait ExpressionExtensionTrait {
       attributeSeq: Seq[Attribute]): ExpressionTransformer = {
     throw new UnsupportedOperationException(s"${expr.getClass} or $expr is not supported.")
   }
+
+  /** Get the attribute index of the extension aggregate functions. */
+  def getAttrsIndexForExtensionAggregateExpr(
+      aggregateFunc: AggregateFunction,
+      mode: AggregateMode,
+      exp: AggregateExpression,
+      aggregateAttributeList: Seq[Attribute],
+      aggregateAttr: ListBuffer[Attribute],
+      resIndex: Int): Int = {
+    throw new UnsupportedOperationException(
+      s"Aggregate function ${aggregateFunc.getClass} is not supported.")
+  }
 }
 
 case class DefaultExpressionExtensionTransformer() extends ExpressionExtensionTrait with Logging {