Abstract: Aiming at applications in space which has environmental features of microgravity, narrow room and limited power resource, a biochip-based PCR device and an optimized PID algorithm for its temperature control were designed and implemented. A set of thermoelectric cooler was adopted as the substrate, biochip technology was used to design the PCR reaction zone and a low power MCU was used to construct the control circuits of the device. On the basis of PID algorithm which controlled the temperature of reaction process, a Kalman prediction mechanism was adopted to reduce the power consumption. Test results indicate that thedevice has the temperature deviation less than 0.5℃ and the average power lower than 3.5 W, which can meet the application requirements of PCR experiments in space.