A halogen heater control apparatus of a microwave oven and a method thereof, comprises a plurality of halogen heaters which are connected to a utility AC power source, and a halogen heater switching unit. The halogen heater and incrementally alters infrared wavelengths from the halogen heater, and a microcomputer controls the operation of the halogen heater switching unit. The present invention is capable of optimum foodstuff heating and cooking by incrementally altering and controlling the infrared wavelengths from the halogen heater by controlling the utility AC power source duty cycle to the halogen heater in accordance with control signals generated by the microcomputer.