This paper mainly studies the trajectory tracking control for quadrotor unmanned aerial vehicle (UAV) with unknown time-varying disturbances including model errors, parametric uncertainties and external disturbances such as wind effects. Conventional back stepping control schemes cannot achieve satisfactory performances in handling time-varying disturbances. Improved schemes, such as: integral backstepping, can only compensate the disturbances in a relative slowly way. By introducing disturbance observer technology into the design process. a composite GPI observer-based robust control scheme is developed. Firstly, a generalized proportional integral observer (GPIO) is used to estimate the lumped time-varying disturbances. Secondly, a composite controller combining backstepping control and disturbance estimation method is designed, which is called the BSC+GPIO method. This control method is convenient to implement and the disturbance rejection capability is enhanced by feedforward compensating the estimated value of system disturbances. Simulation results illustrate the good tracking performance and the robustness of the proposed scheme.