A ship-based Electro-Optical Tracking System (EOTS) driven by PMSM through gear system is designed to reduce the effect of ship-swaying caused by winds and waves.The fiber optic gyroscope is used to detect the motion state of EOTS in real time, and the EOTS is stabilized relative to inertial space by servo control unit.Unlike the land-based EOTS, the swaying motion of a ship caused by winds and waves is coupled to the ship-based EOTS, which has a great impact on its tracking performance.A Disturbance Observer (DOB) of the ship-based EOTS is designed to reduce the effect caused by ship swaying, and of the disturbances of backlash, dead zone, friction, system model mismatch, etc.The DOB is introduced to estimate the lumped disturbances of the system, and the estimated value is used in the feed-forward compensation design to improve the disturbance rejection ability.The experimental results show that the proposed scheme can ensure good anti-disturbance ability, which can enhance the control performance of the system.