Because of the influence of rolling in pitch and yaw channel and the varying of aerodynamic parameters, the design of control system of pitch and yaw channel using classical control theory is a challenging task. Autopilots of pitch and yaw channel are designed based on model reference variable structure control for BTT missile whose model is unable to describe exactly. Simulation models of six degree of freedoms based on MATLAB are established to validate autopilots' property and the simulation results are obtained. MRVSC method has a pretty control effect in the case of varying of aerodynamic parameters and coupling of channels.