A method for alignment of a chip in a substrate surface inspection is provided, in which a surface of a substrate including a chip formed therein is inspected by using a beam. The method is characterized in comprising: a step of placing the substrate so that the chip is positioned within a field of view subject to the inspection; a step of measuring a magnification for the detection when the chip is positioned within the field of view subject to the inspection; a step of calculating a size of position error of the chip based on the measured magnification for the detection; and a step of compensating for the position of the chip based on the calculated position error.