The lift of a quad-rotor aircraft is composed of series frequencies related to the rotor speeds. As it will interferes the control of the aircraft, this paper analyzes the effect of high-frequency lift component on the aircraft and gives an inhibiting method for the lift fluctuation. Firstly, the dynamic model of quad rotor aircraft was established by Lagrangians method and the relational expression between the high-frequency lift component and the disturbance of aircraft angular velocity was obtained. According to the previous analysis, the angular velocity feedback loop was joined a Kalman filter for colored noise to restrain the disturbance of angular velocity acting on the controller. A prototype was designed. The testing results show when the proposed method is used in hovering control of the quad rotor aircraft, the control variable fluctuations decrease by 50% and the high frequency control volume attenuates to under -17 db as compared with that of traditional PID method, respectively. The method of this paper effectively solves the effect of lift fluctuation on the quad rotor aircraft and improves the efficiency of control.