A microheater was established by embedding magnetic nanoparticles into PDMS (MNP-PDMS). MNP-PDMS generated heat under an AC magnetic field and the temperature was controlled by varying the magnetic particle content and the magnetic field intensity. In this study, the MNP-PDMS chip was demonstrated to amplify the target DNA (732 bp) with > 90% efficiency compared to the conventional PCR thermocycler, and exhibited good performance in regards to temperature control. This system holds great promise for reliably controlling the temperature of thermal processes on an integrated microchip platform for biochemical applications.