Based on backstepping technique, this paper presents a design of any reference trajectory tracking controller for marine surface vessels under unknown time-variant environmental disturbances. The mathematical model of nonlinear surface ship movement includes Coriolis and centripetal matrix and nonlinear damp term. The observer is constructed for providing an estimation of unknown disturbances. It is proved that the designed ship trajectory tracking control law can make the resulting closed loop trajectory tracking system of ship be the globally uniformly ultimately bounded and achieve the object of trajectory tracking, while guarantee the global uniform boundedness of all signals of system. The simulation results on a model ship show that the control force and control torque are reasonable, and the transient state and steady-state performances are satisfactory. The effectiveness of the designed control law is verified.