The invention discloses a transformer machine account data verification system and a method thereof. The method comprises respectively acquiring station equipment machine account information and power station equipment machine account nonstandard information for transmitting to a server; encoding the station equipment machine account information and the station equipment machine account nonstandard information by use of a character string form; carrying out one-to-one character matching on transformer information in the encoded station equipment machine account nonstandard information and transformer information in the encoded station equipment machine account standard information; on the basis that the transformer information matches each other, according to preset ownership relations between transformer stations and transformers, querying and obtaining a transformer machine account list of a corresponding transformer; comparing the transformer attributes of the obtained transformer machine account list to obtain transformer machine account information with different matching degree values; classifying the transformers with the same matching degree value into the same kind of transformers; and storing machine account information of the same kind of transformers in the form of a machine account corresponding table, and ending transformer machine account data verification.