The secondary information transmission method of the intelligent station is changed from the previous cable to the optical fiber transmission mode, which leads to problems such as opaque information transmission and inconvenient defect search. Aiming at these problems, this paper proposes an intelligent early warning and fault diagnosis scheme for the secondary circuit of intelligent substation, and according to the scheme, develops an intelligent early warning and fault diagnosis system. According to the characteristics of intelligent substation information transmission, for the problem that there is no physical link model in the 61850 protocol, the communication units such as switches, devices, optical fibers and cables in the secondary communication physical circuit of the process layer are abstracted and modeled. The physical node grid of the process layer is built in the system. The virtual loop information flow of the communication between devices in the SCD is mapped to the actual physical path, and the secondary loop topology structure combining the physical loop and the virtual loop information is formed. According to the information flow characteristics in the intelligent substation, the intelligent substation secondary loop expert knowledge base is established, and the actual running state of the loop is comprehensively judged by real-time acquisition of the operating state information of the device. Realize intelligent early warning and fault diagnosis of the secondary circuit of intelligent substation, and display it in an intuitive way.