1. A wafer inspecting method comprising: scanning a pattern image of a unit inspection region of a first wafer in a normal state in a first mode with definite inspection conditions, and setting the scanned pattern image as a first reference image; scanning a pattern image of a unit inspection region of a second wafer to be inspected in the first mode, and storing the scanned pattern image as a first detection image; comparing the first reference image and the first detection image, and storing a difference of the images as a first difference image; scanning a pattern image of the unit inspection region of the first wafer in the normal state in a second mode with inspection conditions different from the first mode, and setting the scanned pattern image as a second reference image; scanning a pattern image of the unit inspection region of the second wafer to be inspected in the second mode, and storing the scanned pattern image as a second detection image; comparing the second reference image and the second detection image, and storing a difference of the images as a second difference image; generating a third difference image by calculating a balance between the first difference image and the second difference image; and discriminating a defect from noise by using the third difference image.