Owing to the special economic position and environment protection requirements for shallow water, shallow water acoustic communication becomes a hot research area in recent years. The frequency-hopping (FH) technique being considered as one robust and reliable communication plays a vital role in communication system design, because of the characteristics of shallow water channel, e.g., strong multipath, large fluctuation and fast time-varying. Synchronization processing is a key factor of FH system. In this paper, we introduce a real-time FH-MFSK acoustic communication system; adopt the passive time reversal approach to process synchronization for suppressing the multipath interference of underwater acoustic propagation. The united frame structure which contains passive time-reversal synchronization signal is proposed to reduce the impact of time-varying channel on the communication system. Also Convolutional coding is used to future improve the reliability performance of the system. In addition to experimental studies, we used TMS320C6713 DSP for system design. The laboratory pool tests and a sea trial at Wuyuan Bay, Xiamen were carried out. The experimental results demonstrate that the proposed scheme is particularly suitable for FH acoustic communication in shallow water where the channel characterizes as strong multipath, time-varying, fluctuation and random signal variations.