A simulation experiment system for X-ray pulsar based navigation is setup in order to study the key technologies of X-ray pulsar navigation. The system consists of X-ray pulsar source generator, super sensitive X-ray photon counting detector, charge sensitive amplifier, shaping amplifier, time measurement, X-ray pulse profile reconstruction and pulse time of arrival (TOA) measurement. The system can simulate the X-ray pulsar source with different intensities, period and pulse profile. The TOA of individual X-ray photon is recorded, the pulse profile is reconstructed with these data. And by comparing the measured pulse profile with the standard pulse profile of the X-ray pulsar source generator, the pulse TOA is calculated. The construction and the principle of the simulation experiment system are introduced and experiment results are presented.