A communication scheme is proposed based on spread spectrum combined synthetic-aperture for long- rang acoustic communication in shallow water. The Doppler effect and an effective motion compensation method are analyzed using resampling technique combined with All-Phase FFT (AP-FFT) to perform the frequency and phase accuracy estimation, while eliminating the time fuzzy caused by Doppler. This paper uses the acoustic toolbox to model the acoustic channel for further synthetic-aperture communication simulation. The results show that the motion compensation approach proposed can effectively eliminate Doppler effect due to the relative movement between the two elements especially at a high speed. Consequently, this method achieves the coherent combination of signals transmitted by the virtual sub-arrays, reduces diversity gain loss and improves the communication quality significantly.