This study suggests a new type shaft generating system driven by hydrostatic transmission suitable for small size vessels. Since the shaft generating system is affected ceaselessly by disturbances such as speed variation in pump driving speed and variation in external load, a robust servo control must be implemented to obtain stable electric power with constant frequency. Thus, in this study, a digital robust servo control algorithm is applied to the controller design. By the experiment and the numerical computation, the frequency variation characteristics of the generating system under various disturbances are investigated. Conclusively, it is said that the shaft generating system proposed in this study shows excellent control performances.