Micro flow-through PCR could make not only qualitative analysis, but also quantitative analysis of the water sample. The special heater arrangement allows the implementation of up to 40 cycles on the footprint of a sample. The key factor of PCR instrument is precise temperature control, so the temperature control algorithm occupies an important position in whole system. PID and fuzzy-PID algorithms were designed. The simulation model was constructed and experimented with Simulink of Matlab software．The simulation results showed that overshoot of PID algorithm was 8.5 %, adjustment time was 3.4s, the control accuracy was 0.044℃. Overshoot of fuzzy-PID algorithm was 1.45%, adjustment time was only 1.94s, the control accuracy was 0.015℃. Obviously, fuzzy-PID algorithm would overcome the defect of large overshoot of traditional PID, and the adjustment time was shorter.