As an important part of the smart grid, the smart substation is not only the node of energy transmission and distribution, but also the sending and receiving node of various kinds of information, playing an irreplaceable important role. The secondary system is the central nervous system of the smart substation. While realizing the basic functions of measurement, protection and control, it also has many intelligent advanced application functions. The normal operation of the secondary system is an important guarantee for the safe and stable operation of the power grid. In view of this, the reliability research of the secondary system of smart substation was carried out. Based on the analysis of the structure of the secondary system of the smart substation, the reliability model of the secondary system of the smart substation based on the adjacency matrix is established. The protected sampling trip path is obtained by matrix operation. Based on this, the reliability block diagram is drawn and the protection is calculated. Overall steady state availability. Secondly, the above model is applied to different sampling trip modes such as “network mining network jump”, “network mining straight jump”, “direct mining network jump”, “straight mining straight jump”, etc., taking the main transformer protection as an example to give specific Calculation results. Finally, the model is used to analyze the reliability of localization main transformer protection. The results show that the steady state availability of localization protection is significantly improved compared with conventional smart stations.