A method and a system for confirming e-mail authenticity and a non-transitory storage medium thereof are provided. A sender electronic device produces a data fingerprint based on mail content of an e-mail, inserts the data fingerprint into the e-mail, and transmits the data fingerprint and the mail content to a data storage device to be stored. A receiver electronic device obtains the data fingerprint from the e-mail and acquires, based on the data fingerprint, the corresponding mail content from the data storage device. If the corresponding mail content is not stored in the data storage device or the acquired mail content does not accord with the mail content of the received e-mail, the receiver electronic device marks the e-mail as counterfeit.