A Hybrid Automatic Repeat reQuest (HARQ) method and an apparatus in a communication system are provided. The method includes receiving, by a Subscriber Station (SS), first data from at least one first member Base Station (BS) among member BSs of a cooperative cell, when the cooperative cell is configured with the member BSs to provide a communication service to the SS, generating a response signal indicating a reception result of the first data, and transmitting the response signal to at least one predefined second member BS from among the member BSs. The member BSs include a master BS for controlling communication of the member BSs and at least one slave BS for communicating with the SS under the control of the master BS.