In the past, the fault diagnosis method can only find out the malfunction protection and circuit breakers, while can not identify the specific causes of protection and circuit breakers’ incorrect acts. In order to improve system’s safety and reliability, enhance the continuous reliability of power supply and prevent vicious power outage. This paper presents the method of diagnosing the specific cause of substation fault by using fault tree. Firstly, the paper introduces the theory of fault tree analysis method ,then based on the understanding of the meaning of the fault alarm signal, this paper builds the fault tree of circuit breaker and protection to show the reasons at all levels of this three substation failure, and analyse qualitatively and quantitatively. In the end, this paper verifies the validity of the program through actual examples.