The accuracy and real-time of modern missile flight control system of traditional aerodynamic can not be satisfied. In this paper a new method is presented to improve the accuracy and real-time of missiles under this condition. First of all, a missile sub-channel model of the dynamic equations and steering gear is established, then based on the established model, using PID controller to control steering gear and three channels of missile pitch, yaw, roll respectively which is called missile sub-channel PID control method, and finally making use of MATLAB/Simulink to complete the simulation. Simulation results show that compared with traditional aerodynamic control system, this method can reduce the response time of aerodynamic missile and enhance the stability of the control system obviously.