The invention discloses a substation area differential protection method for an intelligent substation, which comprises a big differential protection mode taking the substation as the principal thing, and more than two small differential protection modes taking the substations as the principal things; the big differential protection mode serves as a starting element, any one small differential protection mode serves as an action element; when the two conditions are satisfied simultaneously, the differential protection outputs action; the small differential protection modes are still failure selecting elements; the range of the big differential protection mode is delimitated by high voltage side current of each transformer and all outlet current on the medium voltage side generating line and the low voltage side generating line, of the substation, (not comprising buscouple and segment); the ranges of the small differential protection modes are delimitated by corresponding high voltage side current of the transformer, and all corresponding outlet current on the generating lines connected with main change medium voltage side and low voltage side, (not comprising buscouple and segment). The method not only can thoroughly protect the substation, but also can close the failure transformer in a targeted manner, is small in influence range for the electricity using user, and is particularly suitable for the substation provided with two or more than two transformers to use.