The invention discloses a verification code authentication method and system based on biological characteristics, and the method comprises the steps: transmitting an authentication request, and receiving a verification code; generating a first private key and a first public key according to the acquired biological characteristics; performing hash operation on the biological characteristics to obtain a first private key, and performing elliptic curve encryption on the first private key to obtain a first public key; and signing the verification code according to the first private key, and sending the verification code and the signature information, so as to obtain an authentication result that authentication is completed by the first public key. The biological characteristic value of the user is taken as a private key, thedigital signature is performed on the verification code of the remote server, and the verification code is returned to the remote server; and the remote server authenticates the verification code and the signature information according to the user public key. The biometric features have uniqueness and non-reproducibility, network transmission and key management arenot needed, and the verification code is signed, so that the verification code has authentication, integrity and non-repudiation, and the security of the verification code is improved.