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 testing ships. Recently, the Norwegian Maritime Authority and the Coastal Administration have signed an agreement and started to test autonomous ships in the defined area. Considering recent technology trends and background, in this paper, the authors also try to develop autonomous ship control technologies. In the designed control system, an observer is introduced to estimate unmeasurable system states. Based on the servosystem with state estimator, ship motion control experiment is performed to evaluate control performance using a model ship in water basin.