Recently, polymeric materials have been explored as more versatile alternatives for the fabrication of polymerase chain reaction (PCR) microchips. Poly(methyl methacrylate) (PMMA) is a popular substrate material due to its high mechanical stability, good chemical properties and most importantly, its suitability for cheap and simple CO2 laser ablation. However, it has a low glass transition temperature (Tg) of 105 °C, which is just above the denaturation temperature for PCR, thus the bond integrity is compromised. Polycarbonate (PC) is preferred as a substrate for PCR microchip as it has a higher Tg of 150 °C; but since its thermal properties are not suitable for CO2 laser light, the more expensive excimer laser has to be employed. Here we report a novel hybrid PMMA-PC microchip by bonding a PC cover plate with a PMMA substrate containing microchannel which is fabricated by CO2 laser ablation. This hybrid microchip has improved heat tolerance, such that the bonding integrity is sustained at the denaturation temperature. DNA amplification is found to be more efficiently performed in a PMMA-PC microchip than in a PMMA-PMMA microchip.