A substrate processing apparatus includes a chamber capable of being evacuated, a substrate stage adapted to mount a substrate, a heating unit adapted to be set above the substrate mounting surface of the substrate stage, face the substrate mounted on at least the substrate mounting surface, and heat the substrate by radiant heat without being in contact with the substrate, a shutter adapted to be retractably inserted in the space between the heating unit and the substrate mounted on the substrate mounting surface, and a shutter driving unit adapted to extend/retract the shutter into/from the space. The substrate is mounted on the substrate stage to face the heating unit, the substrate is annealed by heating the substrate by radiant heat from the heating unit, and the shutter is extended into the space between the heating unit and the substrate stage.