The invention discloses a fingerprint encryption-based identity authentication system. The system comprises a user interface, a key interface, a database, a password processing unit, a fingerprint processing unit, a conversion processing unit, a decryption processing unit and an encryption processing unit, wherein the user interface is connected with the password processing unit and the fingerprint processing unit respectively; the password processing unit, the fingerprint processing unit, the decryption processing unit and the encryption processing unit are connected with the conversion processing unit respectively; and the decryption processing unit and the encryption processing unit are connected with the database and the key interface respectively. The invention also discloses an implementation method of the fingerprint encryption-based identity authentication system, which comprises the steps of encryption and decryption. The system and the method have the advantages that: a biological characteristic password can be allowed to be cancelled and can be reset for unlimited times, the safety is high, cross-comparison bugs are prevented, and the like.