The invention discloses an electronic device and a fingerprint authentication method thereof. The fingerprint authentication method comprises the process of reference fingerprint setting and the process of authority authentication. The process of reference fingerprint setting comprises the step of receiving a first fingerprint image sent by a fingerprint collecting unit, the step of converting the first fingerprint image based on a mapping function to produce a distorted first fingerprint image, and the step of storing the distorted first fingerprint image to serve as a reference fingerprint image. The process of authority authentication comprises the step of receiving a second fingerprint image sent by the fingerprint collecting unit, the step of carrying out conversion same as the conversion used in the process of reference fingerprint setting on the second fingerprint image based on the mapping function to produce a distorted second fingerprint image, and the step of determining whether authentication passes or not by comparing the distorted second fingerprint image with the reference image. By means of the electronic device and the fingerprint authentication method thereof, real fingerprints of a user are prevented from being stolen or revealed.