Abstract: Thermal performances of natural convection activated micro polymerase chain reaction（PCR） chips were numerically studied.By calculating the volume fraction of the liquid that satisfied the given thermal cycling,geometrical structures and thermal conditions of the chip were optimized.When the temperature of the top surface was the lower limit of the anneal-extension temperature and the bottom was at the upper limit of the denaturation temperature, an isothermal-side-wall columned chamber with the height to diameter ratio of about 0.275 was demonstrated to be the most appropriate candidate for the present PCR device.Keeping the height to diameter ratio and the volume of the liquid constant,when a solid cirque structure was added in the chamber and the bottom high temperature area reduced from the whole surface to the half radius region,the liquid rested in the denaturation area much shorter than in the anneal-extension area,and the volume fraction of the liquid that satisfied the given thermal cycling was almost not changed.So this condition was more propitious to the PCR process.