Aimed at characteristics of the small unmanned aerial vehicle (UAV) with static stability, the hardware architecture and the control navigation methodology of the flight control system, which was based on ARM and FPGA were designed. The master processor ARM was used to calculate the control and navigation algorithm. The assistant processor FPGA was used to deal with peripheral interface signals. Multiple sensors, MEMS gyros, accelerators, GPS and air pressure sensors, were worked together to enhance the measure precision. The control and navigation channels which were of weaker coupling were also designed in this paper. The UAV was controlled by altitude, heading control loops and navigation methodology to complete the altitude hold and flying over the desire routes. In certain special cases, some safety precautions were taken to enhance flying security. Results of simulation have shown that the control and navigation methodology had a good performance.