Abstract: X ray pulsar can be used for spacecraft autonomous navigation. Pulsar clock can be used to stabilize onboard clock. Utilization in space of X ray pulsar clock is based on high precision determination of pulsar pulse Time of Arrival (TOA) at spacecraft. A method to obtain X ray pulsar pulse profile with individual photon arrival time records by onboard X ray detect system was discussed. In the case that an onboard clock is used as time reference for X ray pulsar timing recorded individual photon arrival time (spacecraft proper time) should be converted to barycentric dynamic time (TDB). Doppler effect due to orbit velocity of spacecraft during observation period may blur observed pulse profile. To mitigate smearing effect to pulse profile further transformation of recorded photon arrival time to Solar System Barycenter (SSB) is required using estimated approximate spacecraft position by spacecraft dynamics. Then obtained X ray pulsar pulse profile is compared with its standard template pulse profile to derive an observed pulse arrival time. Algorithm of determining X ray pulsar TOA at spacecraft with high precision was reviewed. Detailed analysis method to determine TOA in Fourier frequency domain was introduced and compared to analysis method in time domain.