With the development and improvement of intelligent substation, the system structure becomes more and more complex. Many factors lead to the reduction of the reliability of intelligent substation relay protection system. Therefore, the reliability analysis of intelligent substation relay protection becomes more and more important. Due to the need of reliability analysis, a method of reliability analysis of intelligent substation relay protection based on system structure is proposed. Firstly, the reliability block diagram method is used to model the relay protection system of intelligent substation, and the contact matrix method is used to find the minimum path set in the network system. Secondly, the minimum path set disjoint method is introduced to analyze the reliability of the protection system, and a reliability analysis of relay protection system in intelligent substation is conducted based on system structure. Compared with the existing traditional analytical method and simulation method, the method proposed in this paper has a clear flow, which is convenient to find the wrong links in the modeling process. It can clearly express the logical relationship between the intelligent components in the system structure, and it is convenient to find the components in the important position of the relay protection system, so that the reliability analysis becomes concise and intuitive, and this method avoids a large number of repeated calculations, and the accuracy of the calculation results is as well as guaranteed.