In recent years, polymerase chain reaction (PCR) has been used extensively in DNA duplications and biological examinations. To shorten the reaction time, Kopp in 1998 disclosed a continuous-flow PCR chip to reduce the original reaction time from 3 hours to 18 minutes. This research utilizes the continuous-flow PCR chip for the blueprint and the ANSYS for the thermal conduction analysis to provide the simplest design of the manufacture process and optimize the effect of PCR. After the commercial PCR experiments have showed the feasibility of a dual temperature PCR, the dual temperature reaction mechanism is redesigned as to reduce the number of temperature zones and simplify the structural and control variables. For the manufacturing processes such as rinsing, coating, etching, and chip integration, we conducted experiments and tests to find the best recipe and manufacturing process for the production.