In this work, thermal design of a PCR chip for LOC is systematically conducted. From the numerical simulation of a PCR chip based on the finite volume method, how to control the average temperature of a PCR chip and the temperature difference between the denaturation zone and the annealing zone is presented. The average temperature is shown to be controlled by adjusting heat input and a cooler as well as a heater is shown to be necessary to obtain three individual temperature zones for polymerase chain reaction. To reduce the time required, a heat sink for the cooler is not included in the calculation domain for the PCR chip and heat sink design is conducted separately by using a compact modeling method, the porous medium approach.