Abstract: In order to verify the real-time and applicability of the X-ray pulsar navigation algorithm in the space-borne computer environment,an of the X-ray pulsar navigation prototype based on the FPGA + DSP architecture is designed. The FPGA in the navigation prototype is used for logic control and photon data storage. The DSP is used to convert the received photon data,pulse folding,pulse data inter correlation processing,data interpolation and least squares filtering algorithm. A semi physical simulation platform for X-ray pulsars navigation is built to verify the prototype. The system uses residual error of TOA as observation quantity and combines orbital dynamics equation and filtering algorithm to realize navigation and positioning of spacecraft. The simulation results show that the position error is better than 10 km and the speed error is better than 1 km/s.