In a substrate cooling apparatus for cooling a substrate placed on or adjacent a cooling plate having Peltier elements, the substrate is cooled quickly by controlling the Peltier elements to cool the cooling plate to a second set temperature below a target temperature to which the substrate is to be cooled, and switching control of the Peltier elements at a predetermined time after the substrate is placed on or adjacent the cooling plate, to increase the temperature of the cooling plate to the target temperature. Alternatively, the substrate may be cooled quickly by controlling the Peltier elements to cool the cooling plate to a predetermined temperature, controlling the Peltier elements at a normalized maximum cooling output when the substrate is placed on or adjacent the cooling plate, determining, when the cooling plate reaches a peak of temperature increase, a lower limit temperature related to the peak of temperature increase, and switching control of the Peltier elements, when the cooling plate reaches the lower limit temperature, to bring the cooling plate to the target temperature.