Due to the complexity and unpredictability of sea environment, the reliability of dynamic positioning systems of ships has been paid much attention. A robust fault-tolerant control problem for the dynamic positioning system of ships with thruster faults is studied. Firstly, a uniform thruster fault model is established to universally describe different thruster fault cases such as loss-of-effectiveness, stuck and outage. Then, without requiring any fault detection and isolation (FDI) mechanism and the upper and lower bounds of the fault information, an adaptive sliding mode controller is designed where the fault information and unknown external disturbances are estimated online through the adaptive mechanism. With the help of the Lyapunov stability theory and sliding mode control theory, the uniformly ultimate boundedness of all signals in the closed-loop dynamic positioning system of ships can be guaranteed by using the proposed control law. Finally, the simulation is carried out through an overactuated ship model and the results demonstrate the effectiveness of the proposed design control method.