MBD was a creative, efficient development paradigm with long term future for more and more complex embedded controller development. Adopting MBD had great significance for improving the autonomous development ability of missile-borne flight controller development department. In this paper, a certain type of missile borne flight controller hardware was taken as the target platform, according to the model based design and development process, the product level software development of missile borne aircraft was realized. The output results and simulation results of flight controller object were compared and validated, which showed the applicability and efficiency of mod-el-based design in the development of embedded controller.