diff --git a/backends-clickhouse/src/main/scala/io/glutenproject/execution/CHHashAggregateExecTransformer.scala b/backends-clickhouse/src/main/scala/io/glutenproject/execution/CHHashAggregateExecTransformer.scala
index 2ebb80469e46..ad997843eee6 100644
--- a/backends-clickhouse/src/main/scala/io/glutenproject/execution/CHHashAggregateExecTransformer.scala
+++ b/backends-clickhouse/src/main/scala/io/glutenproject/execution/CHHashAggregateExecTransformer.scala
@@ -327,8 +327,19 @@ case class CHHashAggregateExecTransformer(
       ConverterUtils.genColumnNameWithExprId(resultAttr)
     } else {
       val aggExpr = aggExpressions(columnIndex - groupingExprs.length)
+      val aggregateFunc = aggExpr.aggregateFunction
       var aggFunctionName =
-        AggregateFunctionsBuilder.getSubstraitFunctionName(aggExpr.aggregateFunction).get
+        if (
+          ExpressionMappings.expressionExtensionTransformer.extensionExpressionsMapping.contains(
+            aggregateFunc.getClass)
+        ) {
+          ExpressionMappings.expressionExtensionTransformer
+            .buildCustomAggregateFunction(aggregateFunc)
+            ._1
+            .get
+        } else {
+          AggregateFunctionsBuilder.getSubstraitFunctionName(aggregateFunc).get
+        }
       ConverterUtils.genColumnNameWithExprId(resultAttr) + "#Partial#" + aggFunctionName
     }
   }
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 3e2e44426e23..76ec0d7ad1fb 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
@@ -46,17 +46,17 @@ case class CustomAggExpressionTransformer() extends ExpressionExtensionTrait {
     aggregateFunc match {
       case CustomSum(_, _) =>
         mode match {
-          case Partial =>
+          // custom logic: can not support 'Partial'
+          /* 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 =>
+            reIndex */
+          case Final =>
             aggregateAttr += aggregateAttributeList(reIndex)
             reIndex += 1
-            reIndex */
+            reIndex
           case other =>
             throw new UnsupportedOperationException(s"Unsupported aggregate mode: $other.")
         }
@@ -74,10 +74,12 @@ case class CustomAggExpressionTransformer() extends ExpressionExtensionTrait {
           Some("custom_sum_double")
         }
       case _ =>
-        throw new UnsupportedOperationException(
-          s"Aggregate function ${aggregateFunc.getClass} is not supported.")
+        extensionExpressionsMapping.get(aggregateFunc.getClass)
+    }
+    if (substraitAggFuncName.isEmpty) {
+      throw new UnsupportedOperationException(
+        s"Aggregate function ${aggregateFunc.getClass} is not supported.")
     }
-
     (substraitAggFuncName, aggregateFunc.children.map(child => child.dataType))
   }
 }
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 f38cb712160f..d70010957bec 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
@@ -16,8 +16,9 @@
  */
 package io.glutenproject.execution.extension
 
-import io.glutenproject.execution.{CHHashAggregateExecTransformer, GlutenClickHouseTPCHAbstractSuite, HashAggregateExecBaseTransformer, WholeStageTransformerSuite}
+import io.glutenproject.execution._
 import io.glutenproject.substrait.SubstraitContext
+import io.glutenproject.utils.SubstraitPlanPrinterUtil
 
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.catalyst.FunctionIdentifier
@@ -81,18 +82,27 @@ class GlutenCustomAggExpressionSuite extends GlutenClickHouseTPCHAbstractSuite {
     // Final stage is not supported, it will be fallback
     WholeStageTransformerSuite.checkFallBack(df, false)
 
-    val aggExecs = df.queryExecution.executedPlan.collect {
+    val planExecs = df.queryExecution.executedPlan.collect {
       case agg: HashAggregateExec => agg
       case aggTransformer: HashAggregateExecBaseTransformer => aggTransformer
+      case wholeStage: WholeStageTransformer => wholeStage
     }
 
-    assert(aggExecs(0).isInstanceOf[HashAggregateExec])
+    // First stage fallback
+    assert(planExecs(3).isInstanceOf[HashAggregateExec])
+
     val substraitContext = new SubstraitContext
-    aggExecs(1).asInstanceOf[CHHashAggregateExecTransformer].doTransform(substraitContext)
+    planExecs(2).asInstanceOf[CHHashAggregateExecTransformer].doTransform(substraitContext)
 
     // Check the functions
     assert(substraitContext.registeredFunction.containsKey("custom_sum_double:req_fp64"))
     assert(substraitContext.registeredFunction.containsKey("custom_sum:req_i64"))
     assert(substraitContext.registeredFunction.containsKey("sum:req_fp64"))
+
+    val wx = planExecs(1).asInstanceOf[WholeStageTransformer].doWholeStageTransform()
+    val planJson = SubstraitPlanPrinterUtil.substraitPlanToJson(wx.root.toProtobuf)
+    assert(planJson.contains("#Partial#custom_sum_double"))
+    assert(planJson.contains("#Partial#custom_sum"))
+    assert(planJson.contains("#Partial#sum"))
   }
 }