With the increasing development of information science and technology and the vigorous use and promotion of new technologies, profound changes have taken place in all aspects of our daily life. With this huge change, the IoT industry was born. And it analyzes and processes the large amount of data generated between them, and finally, it helps the development of the economy. The RFID system studied in this paper is the radio frequency identification system, which is an automatic signal identification system. The relationship between the RFID system and the Internet of Things is that the former will obtain a large amount of Internet of Things information data by identifying the Internet of Things. However, it is difficult to guarantee the analysis and processing of data and the security of data in the RFID system. This paper aims to study the effective processing and security guarantee of a large amount of data obtained by the RFID system after processing the identification of the Internet of Things. It is expected to overcome the problems of conventional related art. This paper proposes the encryption technology for the Internet of Things RFID system, as well as the corresponding algorithm, and establishes a processing system for information data. The experimental results of this paper show that the cryptographic mechanism run by the algorithm PECC has better security performance compared with other cryptographic mechanisms, and its computational complexity can be reduced by 28.35%.