A pattern inspection method includes: scanning an inspection substrate, to be inspected, to detect a secondary electron group emitted from the inspection substrate due to irradiation with the multiple beams; correcting individually distortion of a first region image obtained from a detection signal of secondary electrons corresponding to a corresponding first region for each beam of the multiple beams; correcting distortion of a corresponding second region image corresponding to a second region larger than the first region for each of the second region images, using data of each of the first region images in which the distortion of the corresponding first region image has been corrected; and comparing an inspection image to be inspected, in which the distortion of each of the plurality of second region images has been corrected, with a reference image of a same region to output a result thereof.