Atomic clock is the core component of navigation satellite payload, playing a decisive role in the realization of positioning function. So the monitoring for anomalies of the satellite atomic clock is very important. In this paper, a complete autonomous monitoring method for the satellite clock is put forward, which is, respectively, based on Phase-Locked Loop (PLL) and statistical principle. Our methods focus on anomalies in satellite clock such as phase and frequency jumping, instantaneous deterioration, stability deterioration, and frequency drift-rate anomaly. Now, method based on PLL has been used successfully in China’s newest BeiDou navigation satellite.