An apparatus for heat treating a substrate includes a substrate holder unit including a substrate stage on which a substrate is to be placed and which is made of one of a carbon and a carbon covered material, and a heating unit which is provided above the substrate stage and includes a heat dissipation surface opposing the substrate stage, and heats the substrate placed on the substrate stage in noncontact therewith radiation heat from the heat dissipation surface. In addition, a chamber contains the substrate holder unit and the heating unit, and an elevating device vertically moves at least one of the substrate holder unit and the heating unit in the chamber to bring the substrate stage and the heat dissipation surface of the heating unit close to each other or apart from each other. The substrate holder unit includes a radiation plate which is arranged under the substrate stage at a gap therefrom, and a reflection plate which is arranged under the radiation plate at a gap therefrom.