X-Ray pulsars/SINS integrated navigation is one of the effective means to extend the application scope of pulsars navigation, and it is also a feasible project of the application of pulsars navigation in the future. When the clock error drifts with time, the Pulsars/SINS Integrated Navigation will be affected. In this paper, the clock error is extended as the state variable, thus a new clock error control algorithm of X-Ray pulsars/SINS integrated navigation is proposed. Results show that the new algorithm can well control the clock error and guarantee the navigation precision of pulsars/SINS integrated navigation, so the new algorithm is referable to the application of navigation based on X-Ray pulsars.