The invention discloses an intelligent substation process layer physical link fault diagnosis method, and relates to the field of intelligent substations. The method comprises the steps of analyzing an SCD file, and obtaining related information of a logic link of a process layer of a whole station and switch configuration information; Obtaining a path node set of a whole station process layer logic link; Analyzing the chain scission signal, obtaining information related to the chain scission signal, and preliminarily screening out a path node set possibly having problems based on the information; Traversing other non-triggered chain scission signals; based on process layer message information related to the triggered chain scission signal, combining with network message analysis; path nodes possibly having problems are further eliminated based on the starting point port power information, the end point port power information and other means of the logic link related to the triggered broken link signal, and the rest path node sets are ranked according to the probability to obtain a final diagnosis result. On the basis of probability statistics, the fault diagnosis range is furtherreduced, and the positioning accuracy is enhanced.