A Si-based miniaturized device for the polymerase chain reaction (PCR) has been developed. The device has Pt temperature sensors and heaters integrated on top of the reaction chamber for real-time accurate temperature sensing and control. Reaction temperature of the device is digitally controlled to achieve a temperature accuracy of +/-0.025 degrees C. The effects of PCR protocol optimization on the amplification performance of the surface-passivated chip reactor have been investigated in detail and quantitatively compared with that of the conventional thermal cycler. In this study, four traditional Chinese medicine genes including Fritillaria cirrhosa, Cartharmus tinctorius, Adenophora lobophilla, and Stephania tetrandra are used as model template. With appropriate chamber surface treatment (chlorotrimethylsilane/polyadenylic acid or SiO2 coatings), the device demonstrates amplification as efficient as that in the conventional thermal cycler at optimized MgCl2 concentration. The amplified DNA has concentration higher than 27 ng/microL, which is sufficient for subsequent on-chip analyses and detection. Experimental results reveal the importance of inclusion of BSA for an efficient amplification in the SiO2-passivated device and the excellent reusability of the device with a simple cleaning step.