Abstract: A PCR（Polymerase Chain Reaction） microchip was designed and fabricated on a silicon wafer. The temperature characteristics of the chip were simulated using CFD-ACE⁺. Natural convective and radiative heat transfer were taken into account as the boundary conditions. The simulation was mainly used to analyze the temperature distribution of the sample and the rate of heating and cooling. The analysis results prove that the chip has higher temperature rising and cooling rates, and temperature distribution of the sample can meet the requirement of the PCR. By combining peripheral thermal control system, the GUS gene is successfully amplified in chip.