An apparatus and method of processing handover of a mobile relay station (MRS) in a cellular communication system using a multihop relay scheme is provided. The handover processing method includes transmitting, by the MRS, a handover request message containing child node information to a serving BS when handover is required; making, by the serving BS, an adjacent node list by collecting handover-related information from adjacent nodes to which the MRS is able to be handed over when the handover request message is received; transmitting, by the serving BS, a handover response message containing the adjacent node list to the MRS; and determining, by the MRS, a handover target node based on information contained in the handover response message and transmitting a handover indication message containing the target node to the serving BS. By suggesting the handover method of the MRS in the multihop relay system, it is possible to provide uninterrupted communication to the MRS and its child node in the service area of the MRS.