Abstract: Fiber bragg grating sensors, which are widely used in health monitor system as high-performance intelligent sensor, are an important tool for Polymerase Chain Reaction (PCR) system. The cycling reactions of the system include three major steps: Denaturation, Annealing and extension and the program design in this paper is focus on the application program in order to achieve precise temperature control, friendly user interface and extremely low-power operation. However, the most commonly measuring method using FBG to get the date effectively is to obtain the wavelength shift information at maximum reflectivity, according to the linear relationship between the wavelength shift and the temperature applied to the axis of the FBG. The inputting signals of thermo-block of the system are constructed with intelligent sensors from a block with 96 narrow tube positions and data storage of the system which are transmitted from Fiber Bragg Gratings is realized in the system. The successful operation is dependent upon its reliable operation under high-precise temperature operating conditions besed on Fiber Bragg Gratings. The experimental results demonstrate that the proposed method is stable and efficient.