Recently, the performance of the new-generation BeiDou Navigation Satellite System (BDS) satellite clocks has attracted considerable attention. There are two types of BDS clocks developed in China—namely, the new rubidium (Rb-II) and passive hydrogen maser (PHM)—and these can affect positioning, navigation and timing (PNT) services. In this paper, to comprehensively evaluate and analyze the performance of BDS satellite atomic clocks, the physical characteristics are exhibited, including phase, frequency, frequency drift and noise. The physical characteristics are applied to detect the switching of satellite clocks. The frequency stability of atomic clocks is assessed by overlapping Allan deviation (ADEV) and overlapping Hadamard deviation (HDEV). The periodic characteristics of satellite clock bias data are studied through spectrum analysis. Based on 550 day precision satellite clock bias data provided by Wuhan University, China, experiments were performed, focusing on the performance of the Rb-II and PHM clocks installed on BDS-3. Some valuable conclusions are obtained: (a) the BDS-3 satellite clocks perform better than BDS-2. The root mean square value of the frequency drift of BDS-3 satellite clocks is enhanced by 41% compared to BDS-2. The noise of BDS-3 is 0.216 ns, which is 55% better than BDS-2. (b) The frequency stability of BDS-2 satellite clocks is worse than that of BDS-3. The mean daily stability of BDS-2 and BDS-3 satellite clocks by ADEV is 5.29 × 10−14 and 5.36 × 10−14, respectively, while that with HDEV is 2.35 × 10−14 and 0.70 × 10−14. For PHM clocks, the stability at 10 000 s with ADEV and HDEV is 2.29 × 10−14 and 2.25 × 10−14, respectively, while the daily stability is 0.77 × 10 −14 and 0.67 × 10−14, respectively. (c) BDS geostationary orbit (GEO) and inclined GEO satellite atomic clocks have multiple significant periodic terms while the medium earth orbit satellite clocks only own one or two, which are related to the corresponding satellite orbital periods.
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