Abstract: An apparatus and method for cooling a thermopile of a microwave oven which is capable of achieving a desired automatic cooking operation by effectively preventing the thermopile from being heated beyond a predetermined level irrespective of the change of the temperature of a heating chamber, wherein the apparatus includes a cooling fan provided at a bottom portion of an electrical components mounting compartment, an air duct provided above the cooling fan for selectively guiding outside air drawn in by the rotation of the cooling fan through a suction inlet to flow either to the inside of the electrical components mounting compartment, or to an upper portion of a heating chamber, and cooling air flow guides attached on the upper surface of the heating chamber, for guiding the cooling air flowing to the upper portion of the heating chamber to be moved towards a thermopile thereat.