A method of manufacturing a semiconductor device bakes a first semiconductor substrate on which a sacrifice film is formed in a reaction chamber to preliminarily coat an inner wall of the reaction chamber with a component of a gas generated by the sacrifice film, and bakes a second semiconductor substrate on which a predetermined film including the same component as that of the sacrifice film is formed in the preliminarily coated reaction chamber, while irradiating electron beams on the predetermined film to change quality of the predetermined film.