An adaptive tracking control method is proposed for the problem of multiple unmanned aerial vehicles(UAVs) tracking desired trajectory under the condition that the coefficients of velocity channel and heading angle channel of autopilot are unknown. These coefficients of autopilot channels are online estimated so as to deal with the design difficulty caused by the unknown coefficients. To attenuate the effect of external disturbance and interior system error on UAVs control system, a compensator is designed. Moreover, by using the Lyapunov functions, it is proved that the trajectory tracking error can eventually converge to an arbitrary small area. Simulation results demonstrate the effectiveness of the proposed method.