The present invention discloses a fingerprint authentication method and a system. The method comprises an authentication step of generating a pair of keys according to the authentication request of a client, wherein the keys comprise a public key and a private key, a sending step of sending the public key to the client, a receiving step of receiving the encrypted data which is generated and sent by the client according to the public key, a decryption step of using the private key to decrypt the encrypted data to obtain decrypted data, and a matching step of matching the locally stored data information and the decrypted data. According to the fingerprint authentication method and the system, the stealing or interpolating of user data in a network transmission process can be prevented, and the safety and reliability of the user data in system certification are ensured.