A pattern inspection method includes scanning a plurality of patterns on a substrate with N charged particle beams and detecting secondary electrons respectively generated from each of the plurality of patterns to acquire N SEM images, determining a distribution of gray level values for each of the acquired N SEM images, selecting M gray levels from the distributions of the N gray levels, selecting a first gray level value from a first one of the M distributions, and comparing it to the corresponding first gray level value of the of the other M−1 distributions, and determining that an abnormality has occurred in the charged particle beam corresponding to the first one of the M distributions when the difference between the first value of the first one of the M distributions and the other M−1 distributions is greater than a predetermined threshold value.