A hardware-in-the-loop simulation system for X-ray pulsar navigation was built in order to do some research for the key technologies in X-ray pulsar navigation field. The system consists of an X-ray pulsar source simulation unit, an X-ray photon receive unit and a navigation estimate unit. The system can simulate X-ray pulsar with different intensities, periods and pulse profiles. The TOA of individual X-ray photon was recorded, and the pulse profile was reconstructed with these data. By comparing the measured pulse profile with the standard pulse profile of the X-ray pulsar source generator, the pulse TOA and the navigation estimation were calculated in the DSP chip. This system is proved effective in test some pulsar navigation algorithms, and can provide reference for the test of feasibility, dynamics and the project application for related X-ray pulsar navigation.