Design of flight control system is a complex system project. In this paper, flight control system for UAV based on MATLAB/Simulink is introduced. The paper also set out core function of mission management in the whole system, formulate the guidance and control law. At the same time, it has an exploratory study of UAV dynamics model, monitor and sensor system, etc. The architecture design of flight control system at the software level is then established. In addition, it provides the rapid prototyping design for flight control system based on MPC Target and xPC target and has a strong engineering application value.