The digitization of total station information in intelligent substation provides the basis for real-time acquisition of relay protection information, however, the reliability analysis of relay protection system in intelligent substation remains in the estimation stage which is lagging behind the real-time operation state. This paper studies the real-time reliability of relay protection device by using the real-time message data of intelligent substation as the online monitoring data of relay protection system. First, from the online monitoring of intelligent substation, this paper classifies the message of intelligent substation and determines the state division of relay protection device. Second, the reliability of relay protection device is analyzed by Markov model, and GO method is used to analyze the reliability of relay protection system based on the characteristics of multimode so as to achieve the real-time reliability analysis function of relay protection device and system. Lastly, this method provides an effective means for the analysis of real-time reliability of intelligent substation protection system is proved by the example of a substation line protection system. This work is supported by National Key Research and Development Program of China (No. 2016YFB0900203).