A stable and reliable time keeping system depends on the integrity monitoring of the atomic frequency standard. This paper reports a scheme for autonomous integrity monitoring of multiple atomic clocks, which combines the frequency standard comparison method and the frequency jump detection method. The frequency standard comparison method uses multi-channel synchronous acquisition technology and digital frequency measurement technology to realize the precise measurement of multiple atomic frequency standards. The frequency jump detection method uses adaptive filtering to predict the relative frequency difference and give an accurate and timely alarm for the abnormal of frequency jump. The results show that the noise floor frequency standard comparator is better than 6.5×10−15 s. For a relative frequency deviation of 2.0×10−6 Hz, the probability of anomaly detection is almost 100 %. The system has high frequency measurement resolution and fast alarm of frequency jump, which can meet the real-time requirements of a time keeping system for the integrity monitoring of multiple atomic clocks.