The invention provides a method for building an in-orbit X-ray pulsar timing model. According to the method for building the in-orbit X-ray pulsar timing model, the problem of data introduced by weak X-ray signal intensity and strong observation platform dynamic condition is effectively solved by organically combining various calculation methods of X-ray pulsar photon arrival time preprocessing, high-precision pulsar autorotation frequency calculation, timing model initial value interval estimation, observation pulse profile reconstruction, high-precision pulse arrival time estimation and robust timing model estimation, ephemeris information such as high-precision pulsar position and time required by X-ray pulsar navigation can be provided, and accurate navigation is realized. The method is suitable for autonomous operation and control of orbiting satellites or constellation of the earth or other planets.