The microfluidic polymerase chain reaction (PCR) biochip cycle circuit geometry is analyzed. For the general non-closed loop circuit paradigm, the feasible temperature zone arrangement is determined; for closed loop circuit paradigm, the heat exchange efficiency of several structural forms are described. Then the excimer laser etching on polymethyl methacrylate (PMMA) plate mechanism is studied, with the etching rate curves listing by experiments. For PCR chip microchannel fabrication, the channel shape and the bottom surface roughness are mainly considered. In the approach, mask shape is designed to fit with the channel shape;laser polishing, near threshold energy etching, heat annealing for stress relief are adopted to promote the channel surface quality. For the problem of chip bonding, the hot press solution is utilized at last. The hot press bonding system is constructed, the optimal bonding parameters is acquired by tests. For driving and controlling of the micro continuous flow, a pecise pneumatic syringe pump system is developed. By utilizing the PCR chip and pump system, an experiment is performed and the amplified product of a 170 bp DNA template chain is successfully acquired.