Abstract: The paper proposed a design scheme of flight control system for aerial robot designed with embedded processor S3C2440 based on ARM9 kernel, introduced composition of the system's hardware structure and design of flight control software based on embedded Linux operation system in details, and described functions division of system software and realization of control strategy. The flight control system makes aerial robotics have functions of remote control and telemetry, instructions processing, attitude stabilized flight and autonomous navigation, which has low cost and high performance.