The invention belongs to the field of underwater acoustic communication and provides a signal synchronization method and system for underwater acoustic communication and an underwater acoustic communication system. According to the method and the system, a start of signal frames is determined by searching for a double peak value of a synchronous evaluation function in the signal frames. Compared with the single-peak evaluation method of the synchronous evaluation function, the invention has the advantages that the interference of random factors upon frame synchronization estimation in the underwater acoustic communication environment is reduced, frame synchronization estimation precision is improved and system bit error rate is decreased.