The navigation computer is designed for initial alignment and navigation computing in strapdown inertial navigation system (SINS). It is the key part of system, and it is made up of chips with high performance and accuracy. By using DSP and FPGA technology, the circuit of navigation computer is designed. Through sequence control and program design, the problems of DSP bootloading, communication, pulse signal counting and navigation computing are solved. According to longtime experimental test, the result shows that the computing error is less than e-10 and speed error is less than±0.5 m/s. The maximum radial error is 0.490 8 nm. And the navigation accuracy is 0.5 nm in 24 hours. The circuit suits the demand of realtime and accuracy for navigation computing. Therefore it is important to navigation system.