The invention provides a monitor system of a hydrogen atomic clock. The monitor system comprises a monitor device and an upper computer platform, wherein the upper computer platform comprises a fault diagnosis expert system module; the fault diagnosis expert system module comprises a man-machine interaction interface for realizing information interaction between a user or an expert and a fault diagnosis expert system, a knowledge acquirer for converting information provided by the user or the expert into corresponding fault diagnosis knowledge, a knowledge base for receiving and storing the fault diagnosis knowledge, a database for storing the actual measurement values of the running parameters of the hydrogen atomic clock, a reasoning machine for carrying out analytical reasoning according to the actual measurement values of the running parameters and the fault diagnosis knowledge to obtain corresponding diagnosis conclusions and solutions, and an explanation machine for explaining the diagnosis conclusions and the solutions obtained by the reasoning machine and transmitting explanation results to the man-machine interaction interface for displaying. According to the monitor system, the fault parts and reasons of the hydrogen atomic clock can be intelligently diagnosed in time and the corresponding solutions are given, so that the reliability of the hydrogen atomic clock is greatly improved.