The present invention relates to an application method for an IED user customized configuration file of an intelligent transformer substation. The intelligent transformer substation comprises a substation control layer device and a process layer device. The method adopts the implementing mode that: firstly, aiming at different functions of an IED, extracting related configuration information of communication between the IED and the devices in the substation from an IEC61850 standard configuration file; and secondly, establishing a mapping relationship between the IEC61850 standard configuration file and IED application function information and forming the IED customized configuration file for the IED to directly read, analyze and apply. According to the application method, the implementing mode of an IEC61850 standard in the IED is simplified, the analytic modeling efficiency of an IED application configuration file is improved, and the debugging period of the IED is shortened.