Aimed at the problems that the reader communication with tags is carried out in insecure wireless channel in the radio frequency identification system, and with the emergence of mobile reader terminals, this makes the communication between the reader and the server unsafe, vulnerable to impersonation attack, eavesdropping attack, middleman attack and other security threats, a two-way authentication protocol for radio frequency identification based on Chinese remainder theorem is proposed. The symmetric encryption and modular operation ways are used to improve the security of information transmission, and the timestamp is adopted to resist the middleman attack in the protocol, and the Chinese remainder theorem is utilized for certificating all sides. Finally, random key update method is used in the keyupdating. The protocol security is verified by formal proof method and routine attack analysis. The protocol of this paper is compared with other protocols in terms of security, calculation and storage. The results show that the protocol is high in security, less in calculation and moderate in storage, and has certain application value in the security field of radio frequency identification.