The present invention provides a method for processing handoff confirm messages. The method includes the following steps: step S102, a serving base station receives a handoff indication message which is from a terminal, and determines the content of the field of the HO confirm type in the handoff confirm message which is to be transferred; and step S104, the serving base station determines whether the service flow information or terminal identifiers are included or not when the handoff confirm messages are transferred to multiple target base stations or target ASNs according to the field of the HO confirm type. The method for processing handoff confirm messages makes handoff among different branches according to different contents in the same controlling procedure, the redundant messages are reduced, and the transmission efficiency of link controlling information and the processing efficiency of the receiving end are improved effectively.