A method and apparatus is provided that controls the handover between distributed units (DUs) (inter-DU handover) in an eNB including a central unit (CU) and a distributed unit (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, for example, smart homes, smart buildings, smart cities, smart cars or connected cars, health care, digital education, retail business, security, safety-related services, etc. The method of performing communication in a communication node of a mobile communication system includes: transmitting, to a source node, a first message instructing handover; receiving, from the source node, a second message including information related to a PDU transmitted to a terminal; receiving, from a target node, a third message related to the reception of a random access preamble of the terminal; and transmitting, to the target node, downlink data, based on the second message, in response to the third message.