The invention discloses a representing method of a corresponding relationship between virtual circuits and physical ports in a secondary circuit graph. Due to the facts that the secondary circuit graph is drawn on the basis of the virtual circuits and the physical ports to represent an interoperation relationship between intelligent devices in an intelligent substation, the representing method of the corresponding relationship between the virtual circuits and the physical ports in the secondary circuit graph has the advantages of representing the virtual circuits between virtual terminals on one piece of graph paper, more importantly, representing a physical port, corresponding to each virtual terminal, of an intelligent device and an access point corresponding to each virtual terminal at the same time, clearly representing a virtual terminal signal transmitted in an optical cable, greatly facilitating debugging and operation management work of a later stage substation, being capable of rapidly finding a fault cause of a physical port when some signal or all signals are out of order, and achieving coupling of the design of a physical layer of the intelligent substation and the design of the logical layer.