A method of manufacturing a substrate, includes: (a) forming the through hole by etching the silicon substrate from a first surface of the silicon substrate by a Bosch process; (b) forming a thermal oxide film such that the thermal oxide film covers the first surface of the silicon substrate, a second surface of the silicon substrate opposite to the first surface, and a surface of the silicon substrate corresponding to a side surface of the through hole, by thermally oxidizing the silicon substrate where the through hole is formed; (c) removing the thermal oxide film; (d) forming an insulating film such that the insulating film covers the first and second surfaces of the silicon substrate and the surface of the silicon substrate corresponding to the side surface of the through hole; and (e) forming the through electrode in the through hole on which the insulating film is formed.