For the huge costs, the space flight experiment cannot be realized in the preliminary step of X-ray pulsar based navigation (XPNAV) research. So, a kind of XPNAV semi-physical simulation experiment system is designed in this paper. This system is composed of two parts: the simulation of pulsar signal and the calculation of navigation parameters. In the first part, the time when X-ray photon arrives at the solar system barycenter is modeled by non-homogeneous Poisson process, then the output pulse of X-ray detector can be simulated by time transformation. In the second part, the navigation information included in the pulses which have been simulated in the first part can be reached by using the Delta-Correction method. This system can be used to simulate four pulsar signals simultaneously, and to study the process of signal processing and parameters calculation of XPNAV at photo level. This system has the advantage of low costs and high simulation accuracy, and provides a reference for the design of prototype in space flight experiment.