A method of manufacturing a semiconductor device, includes the steps of: raising a temperature of a sapphire substrate which is included in the semiconductor device from a room temperature to a preheat temperature of 150° C. to 450° C. and keeping the preheat temperature for a first predetermined time, thereby preheating the semiconductor device; and subsequently raising a temperature of the sapphire substrate from the preheat temperature to a thermal reaction temperature of 500° C. or higher and keeping the thermal reaction temperature for a second predetermined time, thereby performing a thermal reaction treatment of the semiconductor device.