A heat treatment apparatus which enables a heating process for a short time with high reproducibility in a manufacturing process of a MOS transistor manufactured using a semiconductor substrate, and a method of manufacturing a semiconductor device using the heat treatment apparatus are provided. The heat treatment apparatus of the present invention which enables the above heat treatment method is characterized by comprising: a light source; a power supply for turning the light source on and off in a pulse shape; a processing chamber in which the substrate can be irradiated with light from the light source; and a unit for supplying a coolant to the processing chamber and also increasing and decreasing the supply amount.