Abstract: Beidou satellite navigation system has become the main communication system for internet of ships and usually as the only external communication interface in many cases. In this paper, an asynchronous FIFO multi-channel communication model based on shift code with flag was proposed to solve the problems that the multi-channel data assignments and proper message response when there are multiple access devices inquiry information with Beidou terminal. Furthermore, based on proposed model, the communication model has been implemented on a FPGA chip. The simulation results show that the performance of proposed model is both stable and reliable. The asynchronous FIFO multi-channel communication system model has been applied to internet of ships based on the Beidou, and the result proves that it makes a ship to shore communication between on-ship devices and remote shore-based devices effectively.