1. A pattern inspecting method which irradiates light on a sample to be inspected having a pattern, acquires a pattern image to be inspected by detecting reflection light or transmission light from the sample to be inspected and inspects presence/absence of a defect in a pattern of the sample to be inspected based upon the acquired pattern image to be inspected, the method comprising: performing a pixel positional deviation correcting operation, the performing of the pixel positional deviation correcting operation including: superimposing a partial pattern image to be inspected obtained by dividing the pattern image to be inspected acquired from the sample to be inspected and a partial inspection reference pattern image which is obtained by dividing an inspection reference pattern image of the sample to be inspected and corresponds to the partial pattern image to be inspected on one another; correcting a pixel positional deviation between the partial inspection reference pattern image and the partial pattern image to be inspected under such a condition that a sum of squares of level differences between both the partial pattern images becomes the minimum; and performing a processing for the pixel positional deviation correction on all the partial pattern images to be inspected obtained by the division.