The invention provides a smart substation process level secondary circuit fault diagnosis method. The method includes the following steps that a physical connection model is built in a process level network; an SCD file is parsed, and the logic connection relation among devices is analyzed; on the basis of a process level communication topology structure, the logic connection abnormity is mapped to the physical connection according to the related communication link abnormal information, the network topology scanning is conducted, and communication link abnormal nodes are analyzed. According to the smart substation process level secondary circuit fault diagnosis method, the sending and receiving link relation of the process level information is analyzed through the SCD file, the information transmission path of information is searched out in combination with the topological structure, abstract and modeling are conducted on switches, devices and links and communication units in the secondary circuit, the topological structure of the communication network is built, the link scission alarm information of a receiving device is combined, and the fault unit is judged out through comprehensive diagnosis. The whole method is simple, reliable and efficient, contributes to quick communication fault point positioning, and guarantees reliable operation of the secondary circuit of the smart substation.