Methods for processing messages in a wireless communication system including a femto network (FN) including at least one Home NodeB, a core network (CN), a macro network (MN) including a serving base station and a gateway located between the FN and the CN is provided. First, a handover request is received from the Home NodeB or a server of the CN when two mobile devices are communicating. When the handover request is received from the Home NodeB, the gateway transmits a call setup request to the CN to setup a first call path between the gateway and the CN according to the handover request, transmits the handover request to the CN through the first call path to obtain a second call path from the CN to the FN and directs the server to perform the handover request according to the first call path and the second call path.