A method of manufacturing a semiconductor device according to an embodiment of the present invention includes: forming a first insulating film on a semiconductor substrate; forming a mask with an opening of a predetermined pattern in the first insulating film; performing anisotropic etching on the semiconductor substrate with the mask used as an etching mask to form a trench; forming a second insulating film on a surface of an inner wall of the trench with the mask used as a selective oxidation mask; removing the mask; forming a conductive film on the semiconductor substrate to fill the trench with the conductive film; and etching back the conductive film until at least a surface of the semiconductor substrate is exposed.