1. An X-ray examination region setting method of setting an examination region for examining a substrate using an X-rays, the method comprising the steps of: displaying a visible light image obtained by photographing the substrate from a perpendicular direction with respect to a substrate surface; accepting input of information for specifying a range within which a component mounted on the substrate is present in the displayed image; generating three-dimensional reconstruction data from an X-ray fluorography image obtained by performing X-ray fluorography on a three-dimensional region including a region of the component within the specified range; determining information on a position of a wiring connecting the substrate and the component by processing the three-dimensional reconstruction data; and determining, from the determined information on the position of the wiring, a region corresponding to the wiring within the three-dimensional region, and setting the determined region as the examination region.