Polymerase chain reaction (PCR) is a molecular biological method for in vitro amplification of nucleic acids. Our objective was to design a micro-PCR system that included a Rayleigh-Bénard convection PCR chip, measurement circuits, and circuits to control the temperature. A Rayleigh-Bénard convection PCR chip was easily fabricated by using microelectromechanical system technology, and the sample solution could be put in to finish the completed PCR cycling within several minutes. The flow stream, velocity, and temperature profile in a micro-PCR system are important to achieve the successful PCR, but they are not easily observed with an experimental method. Thus, a CFDRC simulation of Rayleigh-Bénard convection PCR was undertaken to determine the above important parameters. The duration of one cycle, the extension time, and total duration of 25 cycles can be calculated to achieve the optimal design. Finally, using agarose-gel electrophoresis, we verified the practicability of this system. The comparison study of PCR experiments performed with a commercial PCR machine and our chips showed that our chips can greatly decrease the duration of the reaction. By comparing the simulation and PCR experiment results with varied designed sizes, a user can set the parameters and computational fluid dynamics results for optimal designs and decrease the total duration of future reactions.