A substrate inspection apparatus includes: an electron beam irradiation device which emits an electron beam and causes the electron beam to irradiate a substrate to be inspected as a primary beam; an electron beam detector which detects at least one of a secondary electron, a reflected electron and a backscattered electron that are generated from the substrate that has been irradiated by the electron beam, and which outputs a signal that forms a one-dimensional or two-dimensional image of a surface of the substrate; a mapping projection optical system which causes imaging of at least one of the secondary electron, the reflected electron and the backscattered electron on the electron beam detector as a secondary beam; and an electromagnetic wave irradiation device which generates an electromagnetic wave and causes the electromagnetic wave to irradiate a location on the surface of the substrate at which the secondary beam is generated.