The progress of the science and technology of aviation and expansion of application are advancing the development of the flight control system of UAV in the direction of high precision, low consumption and miniaturization. A flight control system using Free Scale M56F807 DSP as processor based on neuron PID is designed, which is aimed at the demands of power, cost, reliability and integration from small UAV. The design scheme, hardware and software structure and control strategy are expatiated based on the model of certain type UAV. The difficulty of the algorithm is reduced, and the precision of sampling is improved by using the method of taking a sample and accumulating the average value of the time domain signal. The key techniques related to hardware design are investigated. The system designed has the advantage of simple structure, high reliability and opening. Better experiment results have been made. The digital processing flight control system based on DSP can give the UAV greater mobility, higher flexibility and more extensive applicability.