Disclosed is a method for detecting a virtual secondary circuit of an intelligent substation. The method is characterized by comprising the following steps that A1, a detection module is connected to a network of a process layer; A2, the detection module analyzes an SCD file of the whole substation and conducts logic association; A3, setting of a pre-alarm condition is conducted on associated information; A4, real-time detection is conducted on the virtual secondary circuit; A5, the difference between a set value and an implemented value is judged through pre-alarm operation, and a handling suggestion is provided.