The invention discloses an intelligent substation communication message integrity protection method. An HMAC process that is currently adopted is a fixed key mode, and is secure in a short time, however, in the long term, the risk that a key is cracked is high, and if the key is cracked, the communication security is directly affected. According to the scheme of the invention, a negotiation-basedkey update mechanism is applied in the HMAC process, the integrity authentication and identity authentication of an intelligent substation message can be implemented, and the information security level of a power system can be improved; and according to the scheme of the invention, a number flag bit N is added at the end of the transmitted message, and when the value of N is progressively increased to k, the key is updated, an XOR operation is performed on a new sequence and an initial key, so that new keys can be continuously generated, and the synchronization of key updates is also verified.