The purpose of this study is to analyze the model of a continuous-Flow Polymerase Chain Reaction (PCR) chip with Coventor Ware software. The main idea was to compare the effects of different cross sections of channel and find out the better one for heat transfer. It offered the ability of fast heating and cooling rate when the DNA duplication process happened. Besides, the Top-down and Bottom-up methods to draw relative parameter curves of model was applied on this study.