The invention discloses an intelligent interlocking system of a transformer substation, which comprises an intelligent transformer substation auxiliary comprehensive monitoring system and a transformer substation supervisory control and data acquisition (SCADA) system, and is characterized by also comprising a communication server, an interlocking inference server and an interlocking execution server, wherein the communication server is responsible for communicating with the intelligent transformer substation auxiliary comprehensive monitoring system and the transformer substation SCADA system and receiving real-time data transmitted by the intelligent transformer substation auxiliary comprehensive monitoring system and the transformer substation SCADA system; the interlocking inference server is responsible for reasoning the real-time data received by the communication server, if the real-time data conform to a preset interlocking logic, a correspondent interlocking execution scheme is searched and is outputted; and the interlocking execution server is responsible for converting the interlocking execution scheme transmitted by the interlocking inference server to an action order and automatically controlling an auxiliary device to be accessed to the intelligent auxiliary comprehensive monitoring system according to the action order, and the interlocking execution scheme can trigger a siren and can send a short message and an email to relevant persons. The intelligent interlocking system has an important significance on the aspects such as improving the running safety and reliability of the transformer substation, reducing the energy consumption of the transformer substation and the like.