For wind turbine control systems, if the wind speed changes rapidly, traditional maximum power point tracking strategy will have problems caused by input saturation due to the fast changing desired rotor speed and the large inertia of rotor. This paper proposes a new control strategy to effectively deal with the input saturation problem of wind turbine systems. A double-loop control structure is developed. In the inner loop, a feedback controller is designed to regulate the rotor speed with guaranteed tracking accuracy in spite of various types of uncertainties. In the outer loop, an online trajectory replanning algorithm is implemented to regenerate the desired rotor speed and pitch angle to make the closed-loop system satisfy the input and speed constraints while making the converging speed of the replanned trajectory to the optimal desired trajectory as fast as possible so that the energy loss during transient period is minimized. Simulation result using FAST demonstrates the effectiveness of the proposed strategy.