The hidden fault of the relay protection system is one of the important reasons for the protection malfunction or refusal, and the power system instability. The hidden failure mechanism of relay protection is analyzed. Based on the semantic web technology, the smart substation domain knowledge base and the relay protection hidden fault identification rule base are established on the C Language Integrated Production System (CLIPS) platform. The modeling system of substation primary system, secondary system, communication system and auxiliary system is explained, and the implicit fault identification rule base is further correlated on the basis of this modeling. At the same time, taking a 500 kV intelligent substation as an example, the effectiveness of static characteristics, dynamic characteristics and uncertain hidden fault identification rules and processing strategies are verified by the visualization platform, which provides decision-making basis for intelligent substation operation and maintenance inspection and troubleshooting. This work is supported by Science and Technology Project of the Headquarter of State Grid Corporation of China (No. JBB17201500108) and Science and Technology Project of State Grid Anhui Electric Power Company (No. 52120015007T).