The main fault diagnosis algorithms of traditional substation are based on the protections and breakers. And they have not concerned the influence of abnormal communication network to the stable operation of the intelligent substation. Based on the questions mentioned above, this paper introduces the fault information of the intelligent substation first of all, which contains the static configuration information and the online monitoring information, and then builds the basic model of the whole intelligent substation, and analyses the inference mechanism of the fault diagnosis of the secondary system, and at last tests the correctness of this model through a case.