When diagnosing the fault problem in the relay protection logic link, it mainly depends on the explicit fault characteristics provided by the real-time message information, making the root mean square error of the diagnosis result larger. Therefore, the research on intelligent operation inspection fault diagnosis method of substation relay protection logic link is proposed. Using the three-tier node model framework, the relay protection logic link model is constructed as the basis of fault diagnosis. Through the relay protection fault information system PFIs, the real-time monitoring data of logic link operation status is obtained. Analyze the communication relationship and connection relationship of relay protection equipment, establish the virtual real mapping rules based on the information flow model, and clarify the message transmission path within the logical link. The message transmission port is obtained by using the sink model matrix. According to the virtual real mapping relationship and alarm information, the hidden fault characteristics of the link are extracted and combined with the real-time message information to generate the fault diagnosis results. The simulation results show that compared with the improved D-S evidence theory and rough set-based diagnosis method, the root means the square error of the proposed method is reduced by 17% and 32%.