Along with the continuous development of embedded systems, embedded products take higher requirements on the scale and performance of system software, and contributing to the complexity of control algorithm. So it would take more time and expense to realize the control algorithm. Therefore, traditional design is out of date and cant cope with the modern development rhythm well. While the Model-Based Design, is an efficient design method to deal with complex embedded control systems. It provides a common development and test platform for the engineers. In this paper, we take the power windows control system as example; establish the algorithm model with the Simulink/Stateflow. Then we introduce these process of the control system design which is based on the Model-Based Design method, according to the result of the final experiment, we prove the efficiency of this method, providing a reference for the design of other complex control systems.