Reliability evaluation of secondary system of intelligent substation is an indispensable step to realize condition-based maintenance of smart substation. The existing secondary system reliability evaluation mainly takes the single device or protection function of the smart substation as the evaluation object, without considering the reliability of the process layer devices and links in the secondary system. For this reason, aiming at the bay layer and process layer in the secondary system of smart substation, the network of the bay layer and process layer of the secondary system is divided into protection loop and control loop. Then, based on Markov chain model, the reliability equations of protection loop 、measurement and control loop are established respectively, and the reliability of each loop is evaluated. According to the functional coupling of protection loop and control loop, a reliability evaluation method suitable for bay layer and process layer network is constructed. The example proves that the method proposed in this paper can effectively evaluate the reliability of bay layer and process layer, and provides a basis for condition-based maintenance of secondary system in smart substation.