Along with gradual promotion of intelligent substation construction, a virtual secondary link is difficult to be positioned to a physical link in an intelligent substation at present, and a physical transmission path cannot be positioned accurately and quickly when secondary virtual links such as goose, sv and the like break down, thereby resulting in lagging of troubleshooting. The invention discloses a topological mapping method for secondary virtual and physical links of an intelligent substation. According to the invention, a mode of a corresponding relation of the secondary physical links and the secondary virtual links is generated through carrying out extension on an SCD file, a topological search algorithm is provided, and positioning for a path of the transmitted physical link is realized by the virtual link through a method of traversing port spanning trees. The topological mapping method provided by the invention is not affected by network architecture of the substation, a single network, dual networks or the like, and has very high universality.