A method for managing flow information of a mobile station by a target base station in a communication system is provided. The method includes receiving a ranging request message, which includes a flow identifier for each of flows between a serving base station and the mobile station and a change count indicating the number of times of an addition/change/deletion operation of a corresponding flow for each of flow identifiers, from the mobile station; and transmitting a ranging response message, which includes a validity indicator indicating whether the change count of each of the flow identifiers is valid or not, to the mobile station, wherein, when the validity indicator indicates that at least one change count among change counts for each of the flow identifiers is not valid, the ranging response message includes a list including the at least one change count that is not valid.