The invention discloses an ARQ feedback based resource allocation method for a relay cooperative underwater acoustic communication system. Under the circumstance that the target packet error rate and the status information of an unknown channel at the end of a source node are given, feedback information ACK and NAK (acknowledge/negative acknowledge) of a target terminal are utilized and the situations of relatively complicated underwater environment, relatively severe noise interference and anterior noise amplification by a relay are drawn into consideration to realize dispatching and rate allocation of target users. Simulation results show that compared with a traditional scheme, the scheme provided by the invention can be utilized to obtain relatively low bit error rate (approximate to the performance when the channel status is known) under the condition of relatively low complexity.