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 to 0.30 ns, the short-term prediction error of MEO satellites drops from 0.78 to 0.32 ns, and the media-term prediction error of IGSO and MEO satellites drops from 2.50 to 1.50 ns. Inter-Satellite Links (ISL) with measurement and data communication capabilities is one of the most important ingredient for global BDS system design. With ISL data collected for the five new-generation satellites, this paper compares differences in space signal accuracy, or orbits and clocks in broadcast navigation messages, with or without ISL contribution. Our finding confirms ISL contributes a great deal to the space signal accuracy, in particular when the satellites are not tracked by a regional network. With ISL measurements, the prediction error of MEO broadcast satellite clock parameters drops from 3 ns to within 1 ns when the MEO satellites go into the visual field once more. When ISL measurements join orbit determination as additional observation to L Band code and phase measurements, the orbit determination and prediction accuracy is greatly improved: the radial orbit overlap difference is better than 0.1 m, three-dimensional overlap difference better than 0.5 m and 24 h prediction radial orbit overlap difference is better than 0.2 m, three-dimensional overlap difference better than 1.0 m. Furthermore, with clock measurements obtained with ISL, clock estimates may be decoupled from orbital estimates during orbit determination process for better solutions. A new strategy is proposed in this paper, in which the variation of the satellite clock offsets is constrained and kept as known in orbit determination. With the new strategy, the 4 h prediction UERE drops from 1.04 to 0.82 m.