A GPS/inertial navigation system design scheme is introduced. Combination of DSP and FPGA is used on the navigation board, and micro inertial navigation measuring element --ADIS16405 is used to sample required navigation data. DSP mainly implements navigation calculating based on navigation data, and realizes different navigation algorithms; FPGA in the system plays centeral control role, and not only samples IMU and GPS data, but also synchronize IMU and GPS in the real time, and preprocess and packet the navigation data. This paper also introduces the design of the software on FPGA. Practice proves that the scheme is feasible, and achieves the good balance between the cost, reliability and efficiency.