A pattern inspection apparatus includes a data processing circuitry to input detection data based on a secondary electron from a substrate for each irradiation unit region, where n1×m1 irradiation unit regions in irradiation unit regions configure one of n2×m2 image reference regions configuring an inspection measurement image, to calculate, for each of the n2×m2 image reference regions, a statistic value acquired from the detection data of all the n1×m1 irradiation unit regions in one of the n2×m2 image reference regions, and to define the statistic value as image reference data for the image reference region, and a comparison processing circuitry to receive transmission of the image reference data for each image reference region, and to compare, using a reference image corresponding to the inspection measurement image composed of the n2×m2 image reference regions, the measurement image with the reference image for each image reference region.