The accuracy and stability of the temperature control of the multifunctional biochemical analyzer will affect the accuracy of the biochemical, blood coagulation and specific protein test. In this paper, the design of temperature control system, the CortexM3 controller is adopted in the hardware, combining the temperature acquisition, A/D conversion, set the key, display and so on peripheral circuit, the software using conventional PID algorithm to achieve the incubation tank temperature control. According to the conventional PID algorithm can’t adapt to changes in the external environment of the shortcomings, designed in this paper based on PID neural network BP controller of intelligent temperature control. Through the experiment of temperature test showed that involved based on BP neural network PID controller to realize the instrument in the environment of different areas and countries, can automatically adjust the parameters of the PID algorithm, achieve the repeatability of the selftuning control target, in setting target realizes ±0.1 ℃ C index.