A method of correcting a photomask, comprises preparing a photomask substrate with a mask pattern including a phase shift pattern, forming a reference hole by removing a part of the mask pattern, applying an ion beam from an ion beam source to an area including the reference hole to allow secondary charged particles to be released from the reference hole, obtaining a position of the reference hole by detecting the secondary charged particles by a detector, calculating a positional relationship between the obtained position of the reference hole and a position of a defect of the mask pattern, and correcting the defect by applying an ion beam from the ion beam source to the defect, based on the calculated positional relationship, wherein a pattern of the reference hole, as viewed in a direction perpendicular to a top surface of the photomask substrate, is substantially rectangular, and a longitudinal direction of the rectangular pattern is parallel to a longitudinal direction of the phase shift pattern.