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The atomic clock is the core of the Global Navigation Satellite System (GNSS), which plays an important role in Positioning, Navigation and Timing (PNT) services. However, the long-term characteristics of the global BeiDou navigation system (BeiDou-3) and comparison of satellite clocks performance for the five GNSSs have not yet been revealed. We evaluated and analysed the performance of atomic clocks for BeiDou-3 and other GNSSs using satellite clock offset data. The important contributions are summarised as follows. (1) The phase and frequency sequences of Passive Hydrogen Maser (PHM) and rubidium (Rb) atomic clocks for BeiDou-3 are more stable and continuous than those of the regional BeiDou navigation system (BeiDou-2). The clock offset model precision and average frequency stability at 10,000, 1000, and 100 s for the BeiDou-3 satellite clock offsets are 0.15 ns and 6.8 × 10–14, respectively, exhibiting significant improvements compared with those for BeiDou-2. (2) The performance of cesium (Cs) atomic clocks installed on Global Positioning System (GPS) Block IIF are more inferior than Global Navigation Satellite System (GLONASS), which may be due to the poor level of Cs atomic clock manufacturing technology or obvious noise characteristics. Thus, more attention should be paid to these two satellite clocks. (3) A comparison of various indicators revealed that the satellite clocks for Galileo are the best, followed by BeiDou-3, GPS Block IIF satellites with Rb atomic clocks, Quasi-Zenith Satellite System (QZSS), BeiDou-2, GLONASS, GPS Block IIR, and Block IIR-M. The GPS Block IIF satellites equipped with a Cs atomic clock shows the poorest performance. [ABSTRACT FROM AUTHOR]