A fault diagnosis method using bond graphs in an expert system is proposed for a reactor coolant system. Firstly, the time causality graph and the variable relationship graph are derived from the bond graph. Secondly, the fault signature matrix is obtained by combining the change relationship of fault parameters. Finally, the fault signature matrix is used as the rule of the inference engine design in the expert system for fault diagnosis. In this paper, the key equipment of the reactor coolant system is used to verify the fault diagnosis method of the bond graph expert system, and the path reasoning relationship between alarms is obtained, which can accurately obtain the deep knowledge required by the operators. A new idea for fault diagnosis in a nuclear power plant’s expert system is provided by this method.