A two-way satellite time and frequency transfer(TWSTFT) device equipped in the BeiDou navigation satellite system(BDS)can calculate clock error between satellite and ground master clock. TWSTFT is a real-time method with high accuracy because most system errors such as orbital error, station position error, and tropospheric and ionospheric delay error can be eliminated by calculating the two-way pseudorange difference. Another method, the multi-satellite precision orbit determination(MPOD)method, can be applied to estimate satellite clock errors. By comparison with MPOD clock estimations, this paper discusses the applications of the BDS TWSTFT clock observations in satellite clock measurement, satellite clock prediction, navigation system time monitor, and satellite clock performance assessment in orbit. The results show that with TWSTFT clock observations, the accuracy of satellite clock prediction is higher than MPOD. Five continuous weeks of comparisons with three international GNSS Service(IGS) analysis centers(ACs) show that the reference time difference between BeiDou time(BDT) and golbal positoning system(GPS) time(GPST) realized IGS ACs is in the tens of nanoseconds. Applying the TWSTFT clock error observations may obtain more accurate satellite clock performance evaluation in the 104 s interval because the accuracy of the MPOD clock estimation is not sufficiently high. By comparing the BDS and GPS satellite clock performance, we found that the BDS clock stability at the 103 s interval is approximately 10.12, which is similar to the GPS IIR. A two-way satellite time and frequency transfer (TWSTFT) device equipped in the BeiDou navigation satellite system (BDS) can calculate clock error between satellite and ground master clock. TWSTFT is a real-time method with high accuracy because most system errors such as orbital error, station position error, and tropospheric and ionospheric delay error can be eliminated by calculating the two-way pseudorange difference. Another method, the multi-satellite precision orbit determination (MPOD) method, can be applied to estimate satellite clock errors. By comparison with MPOD clock estimations, this paper discusses the applications of the BDS TWSTFT clock observations in satellite clock measurement, satellite clock prediction, navigation system time monitor, and satellite clock performance assessment in orbit. The results show that with TWSTFT clock observations, the accuracy of satellite clock prediction is higher than MPOD. Five continuous weeks of comparisons with three international GNSS Applying the TWSTFT clock error observations may obtain (TW) the GPS time (GPST) realized IGS ACs in the tens of nanoseconds. Service (IGS) analysis centers (ACs) show that the reference time difference between BeiDou time (BDT) and golbal positoning system more accurate satellite clock performance evaluation in the 104 s interval because the accuracy of the accuracy of the MPOD clock estimation is not sufficiently high. which is similar to the GPS IIR.