The simulation of X-ray pulsar observation signals at spacecraft is of great significance in verifying pulsar signal processing methods and navigation schemes. The efficiency of pulsar signal simulation algorithm can be significantly improved by establishing the relationship between photon arrival time and phase at spacecraft. At present, the frequency change of the received pulsar signal is not considered in the model for the relation between photon arrival time and phase at spacecraft, which leads the calculation accuracy to decrease greatly. To solve this problem, a model for the relation between photon arrival time and phase is established with the first derivative and second derivative of frequency taken into consideration. Based on this model, a new simulation method of observation pulsar signal at a spacecraft is proposed, which not only ensures high efficiency, but also improves the simulation accuracy. The proposed method is verified from three aspects. Firstly, the correctness of the proposed method is proved by comparing the cumulative pulse profile from the simulation data with the standard pulse profile, and the results show that the standard pulse profile can be recovered by the simulation data from the proposed method. Secondly, through the comparison of experimental results with the observational data from RXTE (Rossi X-ray timing Explorer), the correctness of the proposed method is further verified. The experimental comparison results show that the absolute difference in searched frequency between simulated data and observational data for the Crab pulsar is less than 10^–4, which sufficiently validates the method. Finally, the simulation efficiency and accuracy of the proposed method are compared with those of other methods to prove the superiority of the proposed method over the existing methods. The comparison results show that the simulation speed of the proposed method can be increased by up to 3 orders of magnitude compared with that of the iterative method or the method of establishing the real-time photon arrival rate function at the spacecraft, which ensures the high efficiency of the signal simulation algorithm. And comparing with the case without considering the frequency change, the Pearson correlation coefficient is increased by up to 350.0%, significantly improving the calculation accuracy. The proposed method can be used to verify the X-ray pulsar signal processing and navigation algorithms.