Effective host-local system architecture for PCR chips is presented. The functions required for the control of the chips and their partitioning into the host and the local system are qualitatively analyzed. The results indicated that, most functions can be resided in the host to deliver the benefits on the development period, the system cost, and the maintenance. The control system was implemented with PC as the host and the local system was connected by USB interface, obtaining the superior development and the GUI design environment. A PCB-based PCR chip example was constructed and tested to verify the proposed system.