Abstract:   Five new-generation BeiDou Satellite Navigation System (BDS) satellites, including two satellites in the Inclined Geostationary Orbit (IGSO) and three satellites in the Medium Orbit (MEO), have completed deployment on 1st February 2016. The mission of the five new-generation satellites is to validate the new system designs and the new technologies that will successfully expand BDS’s Positioning, Navigation and Timing (PNT) services from regional to global. Responsible to keep time and frequency standards that are used to generate navigation signals, atomic clocks are important payloads onboard BDS satellites. Using data from BDS’ two-way satellite time and frequency transfer system, this paper evaluates performance of those new generation atomic clocks (Hydrogen Maser and Rubidium). Compared to the regional operational satellites onboard atomic clocks, the prediction accuracy of the new-generation onboard atomic clocks is improved. The short-term prediction error of IGSO satellites drops from 0.65 ns to 0.30 ns, the shortterm prediction error of MEO satellites drops from 0.78 ns to 0.32 ns, and both the media-term prediction error of both IGSO and MEO satellites drops from 2.50 ns to 1.50 ns. Time frequency system is an important part of the ground movement control of the new generation test system, which is responsible for the generation and maintenance of the time frequency signal of the new generation test system. Using the data from the new generation test system time and UTC(BSNC), this paper evaluates performance of system time in new generation test system, compared to the regional system time, the performance of new generation test system time is improved, the 1000s stability and day stability compared to the regional system improve about half an order. Central-distributed time and frequency system is the key technology in the new generation test system. Using the two-way data from center note and frontier node, this paper evaluates performance of frontier node time in new generation test system. Results show that the center note frontier note are in good consistent, with the largest value of 0.23 ns.