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 43decfba28b7..3e2e44426e23 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
@@ -21,6 +21,7 @@ import io.glutenproject.extension.ExpressionExtensionTrait
 
 import org.apache.spark.sql.catalyst.expressions._
 import org.apache.spark.sql.catalyst.expressions.aggregate._
+import org.apache.spark.sql.types.{DataType, LongType}
 
 import scala.collection.mutable.ListBuffer
 
@@ -61,4 +62,22 @@ case class CustomAggExpressionTransformer() extends ExpressionExtensionTrait {
         }
     }
   }
+
+  /** Get the custom agg function substrait name and the input types of the child */
+  override def buildCustomAggregateFunction(
+      aggregateFunc: AggregateFunction): (Option[String], Seq[DataType]) = {
+    val substraitAggFuncName = aggregateFunc match {
+      case customSum: CustomSum =>
+        if (customSum.dataType.isInstanceOf[LongType]) {
+          Some("custom_sum")
+        } else {
+          Some("custom_sum_double")
+        }
+      case _ =>
+        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 3a52e0e7b148..f38cb712160f 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
@@ -16,7 +16,8 @@
  */
 package io.glutenproject.execution.extension
 
-import io.glutenproject.execution.{GlutenClickHouseTPCHAbstractSuite, WholeStageTransformerSuite}
+import io.glutenproject.execution.{CHHashAggregateExecTransformer, GlutenClickHouseTPCHAbstractSuite, HashAggregateExecBaseTransformer, WholeStageTransformerSuite}
+import io.glutenproject.substrait.SubstraitContext
 
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.catalyst.FunctionIdentifier
@@ -63,6 +64,7 @@ class GlutenCustomAggExpressionSuite extends GlutenClickHouseTPCHAbstractSuite {
          |    l_returnflag,
          |    l_linestatus,
          |    custom_sum(l_quantity) AS sum_qty,
+         |    custom_sum(l_linenumber) AS sum_linenumber,
          |    sum(l_extendedprice) AS sum_base_price
          |FROM
          |    lineitem
@@ -79,9 +81,18 @@ class GlutenCustomAggExpressionSuite extends GlutenClickHouseTPCHAbstractSuite {
     // Final stage is not supported, it will be fallback
     WholeStageTransformerSuite.checkFallBack(df, false)
 
-    val fallbackAggExec = df.queryExecution.executedPlan.collect {
+    val aggExecs = df.queryExecution.executedPlan.collect {
       case agg: HashAggregateExec => agg
+      case aggTransformer: HashAggregateExecBaseTransformer => aggTransformer
     }
-    assert(fallbackAggExec.size == 1)
+
+    assert(aggExecs(0).isInstanceOf[HashAggregateExec])
+    val substraitContext = new SubstraitContext
+    aggExecs(1).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"))
   }
 }
diff --git a/cpp-ch/local-engine/Parser/example_udf/customSum.cpp b/cpp-ch/local-engine/Parser/example_udf/customSum.cpp
index 12754c858013..66328495d0e2 100644
--- a/cpp-ch/local-engine/Parser/example_udf/customSum.cpp
+++ b/cpp-ch/local-engine/Parser/example_udf/customSum.cpp
@@ -24,4 +24,5 @@ namespace local_engine
 {
 // Only for ut to test custom aggregate function
 REGISTER_COMMON_AGGREGATE_FUNCTION_PARSER(CustomSum, custom_sum, sum)
+REGISTER_COMMON_AGGREGATE_FUNCTION_PARSER(CustomSumDouble, custom_sum_double, sum)
 }
diff --git a/gluten-core/src/main/scala/io/glutenproject/expression/AggregateFunctionsBuilder.scala b/gluten-core/src/main/scala/io/glutenproject/expression/AggregateFunctionsBuilder.scala
index cce8e4c498ea..ab6c13832ae6 100644
--- a/gluten-core/src/main/scala/io/glutenproject/expression/AggregateFunctionsBuilder.scala
+++ b/gluten-core/src/main/scala/io/glutenproject/expression/AggregateFunctionsBuilder.scala
@@ -27,19 +27,30 @@ object AggregateFunctionsBuilder {
   def create(args: java.lang.Object, aggregateFunc: AggregateFunction): Long = {
     val functionMap = args.asInstanceOf[java.util.HashMap[String, java.lang.Long]]
 
-    var substraitAggFuncName = getSubstraitFunctionName(aggregateFunc)
+    // First handle the custom aggregate functions
+    val (substraitAggFuncName, inputTypes) =
+      if (
+        ExpressionMappings.expressionExtensionTransformer.extensionExpressionsMapping.contains(
+          aggregateFunc.getClass)
+      ) {
+        ExpressionMappings.expressionExtensionTransformer.buildCustomAggregateFunction(
+          aggregateFunc)
+      } else {
+        val substraitAggFuncName = getSubstraitFunctionName(aggregateFunc)
 
-    // Check whether each backend supports this aggregate function.
-    if (
-      !BackendsApiManager.getValidatorApiInstance.doExprValidate(
-        substraitAggFuncName.get,
-        aggregateFunc)
-    ) {
-      throw new UnsupportedOperationException(
-        s"Aggregate function not supported for $aggregateFunc.")
-    }
+        // Check whether each backend supports this aggregate function.
+        if (
+          !BackendsApiManager.getValidatorApiInstance.doExprValidate(
+            substraitAggFuncName.get,
+            aggregateFunc)
+        ) {
+          throw new UnsupportedOperationException(
+            s"Aggregate function not supported for $aggregateFunc.")
+        }
 
-    val inputTypes: Seq[DataType] = aggregateFunc.children.map(child => child.dataType)
+        val inputTypes: Seq[DataType] = aggregateFunc.children.map(child => child.dataType)
+        (substraitAggFuncName, inputTypes)
+      }
 
     ExpressionBuilder.newScalarFunction(
       functionMap,
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 d1fc219b7bbb..8542a7fdbc86 100644
--- a/gluten-core/src/main/scala/io/glutenproject/extension/ExpressionExtensionTrait.scala
+++ b/gluten-core/src/main/scala/io/glutenproject/extension/ExpressionExtensionTrait.scala
@@ -21,6 +21,7 @@ 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 org.apache.spark.sql.types.DataType
 
 import scala.collection.mutable.ListBuffer
 
@@ -52,6 +53,13 @@ trait ExpressionExtensionTrait {
     throw new UnsupportedOperationException(
       s"Aggregate function ${aggregateFunc.getClass} is not supported.")
   }
+
+  /** Get the custom agg function substrait name and the input types of the child */
+  def buildCustomAggregateFunction(
+      aggregateFunc: AggregateFunction): (Option[String], Seq[DataType]) = {
+    throw new UnsupportedOperationException(
+      s"Aggregate function ${aggregateFunc.getClass} is not supported.")
+  }
 }
 
 case class DefaultExpressionExtensionTransformer() extends ExpressionExtensionTrait with Logging {