Hidden fault of relay protection system is one of the main causes of blackouts in power grid. The popularization of intelligent substation technology provides new ideas and technical means for fault diagnosis of relay protection.Based on the structure of Smart Substation and taking the hidden fault diagnosis of relay protection system in Smart Substation as the research object, a hidden fault diagnosis method of relay protection system under disturbance excitation is proposed, the existence of hidden fault is judged by the analysis of disturbance, and the feasibility of this method is verified by an example, the results show that this method can diagnose and protect the system, coordination between them to improve the real-time recognition of relay protection status.The research provides a reference for the development of intelligent substation in China.