For the lower safety problem in the "static password + real-time data" authentication modes of WEB cloud storage system, this paper designs an authentication system based on fingerprint identification technology. It uses the authentication model based on fingerprint identification for user identity authentication, improving the authentication security and reliability, and solving the issues of user account illegal access and tampering. It proposes the hybrid encryption algorithm based on symmetric encryption algorithm and asymmetric encryption algorithm which is used as a identity authentication protocol. This method effectively improves the certification efficiency, and realizes the effective transmission of huge amounts of data. The experimental results show that the scheme obtains very good application in the cloud storage identity authentication system.