A method and apparatus are provided that controls the handover between DUs in an eNB including a CU and a DU. The method and system fuses 5G communication systems with IoT technology to transmission data at a high rate after 4G systems. The communication method and system is applied to intelligent services, based on 5G communication technology and IoT related technology. The method includes transmitting, to a source DU of the base station, a first message related to a handover; receiving, from the source DU, a second message for downlink data delivery information related to a PDU transmitted from the source DU to a terminal; receiving, from a target DU of the base station, a third message based on a random access procedure of the terminal toward the target DU; and transmitting, to the target DU, downlink data based on the downlink data delivery information after receiving the third message.