The invention discloses a three-layer graph-based intelligent substation virtual loop visual comparison method. According to the method, comparison of a virtual loop is realized from top to bottom in a graphic mode step by step from three levels of a device, a link and a link passage. The method has the beneficial effects that a comparison graph of the intelligent substation virtual loop is visual, the real-time monitoring is performed on change of virtual loop configuration information in an SCD (System Configuration Description) file caused by a reconstruction and expansion process, the safety, the integrity and the consistency of the virtual loop configuration information are guaranteed to the greatest extent, the current situation that the low-efficiency and fragile virtual loop configuration correctness is guaranteed by means of labor is changed, then the safe operation level of the intelligent substation is guaranteed and improved, the system operation time is shortened, the pressure for putting into operation is reduced, and the maintenance cost in the whole life cycle of the intelligent substation is reduced.