Anti-disturbance control problem is studied for ship dynamic positioning systems with model uncertainties and ocean disturbances under thruster faults. For the ocean disturbance, a stochastic disturbance observer (SDO) is established to give the online estimation. For thruster faults, an adaptive law is used to evaluate, which is obtain from Lyapunov function. For model uncertainties, a robust control term with adaptive technology is used to attenuate it. Then, a composite anti-disturbance control (CADC) strategy is raised by combining disturbance observer-based control (DOBC), adaptive technology, and robust control term, which makes the position and yaw angle of ship reach the desired values. Finally, the simulation example proves the validity of the controller.