Provided are a temperature control method and apparatus for driving a polymerize chain reaction (PCR) chip. In the temperature control apparatus, which is for a polymerize chain reaction chip, PCR chips receive electric power from the outside and generating heat to maintain a predetermined temperature and for outputting actual temperature information to the outside. electric power supply units supply electric power to the PCR chips according to input control signals, and a controller generates the control signals based on control information including pre-established control temperature and control time information and the actual temperature information supplied from the PCR chips in order to supply the control signals to the electric power supply units. In the present invention, it is possible to examine various kinds of DNA at the same time because the temperature control apparatus controls the temperatures of DNA samples at the same time.