The SINS/CNS/GNSS integrated navigation system has many technology advantages, such as complete autonomy, strong anti-jamming ability and high-precision, and has higher demand for navigation computer. Setting out from the demand of navigation computer, a navigation computer which has high precision, high reliability, miniaturization, low cost, low power, based on DSP and FPGA is designed in this paper. Firstly, the system structure diagram is presented, and the main function modules of the system are introduced in detail. Secondly, the basic designing ideas of program are shown. Finally, the MTBF of the computer system according to the data and methods of GJB/Z 299C-2006 are calculated .The practical application results show that the navigation computer system features of processing speed, processing precision, reliability, cost, volume and power satisfy the requirements of the integrated navigation system.