As the core component of navigational satellites, the on-board atomic clock is of key importance for guaranteeing the stable operation of global satellite navigation systems (GNSSs). As GNSSs are modernized, the clocks of several satellites have been changed to support long-term in-orbit operation. Analysis of the performance of on-board clocks is therefore crucial for supporting the positioning, navigation and timing of the satellite navigation system. Most studies involving stability analysis have not paid much attention to performance variation as a consequence of clocks being changed. This motivated our study, in which we analyzed the time domain characterization of on-board clocks from January 2016 to October 2018 to detect the variation. With respect to frequency domain characterization, conventional methods for noise analysis are easily affected by frequent fluctuations and local discontinuities as the averaging time increases. Hence, we propose the lag 1 autocorrelation function method based on overlapping samples to identify the noise of satellite clocks. We find that the time domain stability of the Galileo clock is of the magnitude of 10–13, 10–14 and 10–15 at averaging times of 100 s, 1000 s and 1 d, respectively, which is one order of magnitude better than that of the Russian global navigation satellite system (GLONASS). Moreover, the stability of the passive hydrogen masers on board Galileo shows a certain improvement due to the frequency modulation. The overall performance of the GLONASS cesium atomic clock and the Galileo rubidium atomic frequency standard is stable without any obvious aging in recent years. In terms of the frequency domain characterization, GLONASS clocks are mainly affected by flicker phase modulation noise, white frequency modulation noise and flicker frequency modulation noise, whereas the Galileo clocks are mainly affected by three kinds of frequency modulation noise.

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