The invention discloses a difference comparison system of an intelligent substation configuration file, and aims to solve the technical problem that the normal operation of device equipment is affected since the change of a configuration file in the new construction, reconstruction, extension and operation and overhaul processes of an intelligent substation is hard to distinguish. The difference comparison system comprises a display module, a document data comparison module, a storage module and a server database, wherein the display module is used for displaying a human computer UI (User Interface) interaction interface to display a comparison result of the document data comparison module; the document data comparison module carries out maximum LCS (Longest Common Subsequence) solving on an original file custom structure data sequence and a target file custom structure data sequence and carries out comparison to obtain a comparison result, and the comparison result is subjected to difference coloring and is sent to the display module to be output and displayed; the storage module stores the comparison result and temporarily stores converted original file custom structure data and converted target file custom structure data; and the server database stores the original comparison file and the target comparison file of a user.