In view of the problem of insufficient reliability of redundant intelligent substation area protection during maintenance, failure exit, disaster recovery and other scenarios, a new relay protection architecture of Remote Duplicate Configuration Smart Protection Center (RDCSPC) is proposed. Because it is built in different places, the reliability of its communication system must be considered. In this paper, Markov state space method is used to model each sub-module of RDCSPC communication system. The logical relationship between failure rate and repair rate is determined. The availability expressions of each sub-module and RDCSPC communication system under two networking conditions are obtained. The specific values of reliability index are obtained through the analysis and calculation of an example. The example results show that the communication system based on RDCSPC has high reliability under two kinds of networking. On this basis, the rationality of several substations under the jurisdiction of one RDCSPC is further discussed. This work is supported by National Natural Science Foundation of China (No. 51477090) and Science and Technology Project of State Grid Corporation of China “Key Technique Research and Development of New Architecture Protection of Adapting Substation-Network Form Evaluation Tendency”.