In this study, a ship motion control system design method is introduced for autonomous ships. Some related research results and technologies for autonomous ships have already been developed and applied to ships. For example, the Norwegian Maritime Authority and the Coastal Administration have signed an agreement that allows to test of autonomous ships in the defined area (port to port). Many countries and industries are pursuing to realize the autonomous vessel in the real world. In this paper, the authors try to develop related technology. As basic research, a ship model of the pilot vessel is developed and physical parameters are identified by experiment and simulations. Using the mathematical ship model, a control system is designed and control performance is evaluated by simulations.