Neutral beam injection (NBI) is one of the heating methods in tokamaks. In the process of injection, the neutral particles will not be absolutely absorbed by plasma. The unabsorbed neutral particles penetrate plasma and are shot at inner wall tiles. It will cause the temperature increases of armor tiles that are placed opposite the NBI injection windows. In order to ensure that the armor tiles work during a safe interval, the data acquisition and protection system of infrared thermometer has been developed. The system achieves the functions of isolated transmission, remote monitoring, and fast protection. The response time of data acquisition and protection system is less than 5 μ, and the transmission rate of the system is 5 kHz. The quick response and stability of the data acquisition and protection system have been confirmed in practice.