Abstract The safety and reliability of substations under the background of ‘double carbon’ is the key to ensuring the stable operation of new power systems. As an important part of the new power system, the construction scale of intelligent substations and the scale of the secondary system are constantly expanding, which puts forward higher requirements for the fault diagnosis of the secondary system of intelligent substations. In this paper, we first analyze the Substation Configuration Description (SCD) of the whole station of the intelligent substation and analyze the information of the secondary system of the intelligent substation and the topological relationship of the virtual terminals and virtual circuits. A secondary system fault localization method based on the combination of a diagnostic model and fuzzy fault tree theory is proposed. An intelligent substation secondary system fault diagnosis system is developed, which determines the faulty equipment based on the substation static configuration information, fault characteristic logical relationship, fault diagnosis model, and derivation through an intelligent algorithm. This paper comprehensively analyses the intelligent station secondary configuration, network status information, message information, and other aspects of information in the intelligent substation SCD. Through the real-time tracking of the communication data in the link layer and network layer in the communication system of the intelligent substation, when the optical sign alarm occurs, the accurate positioning of the fault is accomplished through the secondary equipment defect analysis expert system, and then the alarm information is displayed together, and finally, the solution for the fault is given. This study provides a certain scientific basis for the construction of fault diagnosis of secondary systems of intelligent substations in the future.