In this paper, a trajectory tracking control scheme for a quadrotor unmanned aerial vehicle (UAV) under unknown external disturbance and input saturation is developed. This scheme includes the position control system and attitude control one, in which the attitude control system is further divided into the fast loop for angular velocity and the slow one for attitude angle based on time-scale separation principle. Then, an input constrained dynamic surface control scheme combined with a disturbance observer is designed to achieve the total thrust, desired roll, and pitch angle in the position control system. For the coupled attitude system, a dynamic surface control scheme together with generalized model predictive controller (GMPC) is proposed to tackle both the fast loop system and the slow one. Since the unknown external disturbance and input saturation are considered, a sliding mode disturbance observer (SMDO) is further designed to achieve the strong robustness. Finally, some simulation results are presented to show robustness and effectiveness of our proposed tracking scheme.