The comprehensive positioning navigation timing (PNT) system in China is a multi-source information fusion system with BeiDou navigation satellite system (BDS) as a core. The high-precision millisecond pulsar timing can enhance the long-term stability of the BDS time benchmark and maintain a space-time benchmark for future deep-space users. In this paper, a ground-based pulsar time service system is proposed for detecting and improving the time benchmark of BDS. The preliminary designs and functions of the system are outlined. At the same time, the method of establishing space and ground-based pulsar time is studied. The ground radio timing data from the international pulsar timing array (IPTA), the X-ray timing data from the neutron star interior composition explorer (NICER) in space, and the simulation data from the 500-meter spherical radio telescope (five-hundred-meter aperture spherical radio telescope, FAST) for three millisecond pulsars are used to analyze the stability of ground/space-based pulsar time. The research results are as follows. The annual stability of the PSR J0437-4715 ground-based pulsar time based on IPTA data is 3.30 × 10^–14, and the 10-year stability is 1.23 × 10^–15, respectively. The existence of pulsar red noise can reduce the time stability of the pulsar. The annual stability of the PSR J1939+2134 ground-based pulsar time is 6.51 × 10^–12. We find that the accuracy of the pulse time of Arrival(TOA) is an important factor that restricts the stability of space-based pulsar time. Based on NICER space X-ray timing data, the stability of the pulsar time for PSR J1824-2452A is 1.36 × 10^–13 in one year. Finally, the simulation analysis of the FAST’s data without considering the influence of red noise is completed, and we find that the PSR J1939+2134 ground-based pulsar time based on the FAST has an annual stability of 2.55 × 10^–15, a 10-year stability of 1.39 × 10^–16, and a 20-year stability of 5.08 × 10^–17. It demonstrates that the powerful pulsar observation capability of FAST will help to improve the accuracy of ground-based pulsar time and enhance the long-term stability of the comprehensive PNT system time benchmark in China.