An electron beam inspection apparatus includes an analyzing circuit to input design pattern data of design pattern of a semiconductor element, and specify a position of a pattern portion including a feature point, which has previously been set, by analyzing the design pattern data; and a comparison circuit to input information on a specified position of the pattern portion including the feature point, and determine by comparing a secondary electron image and a design substrate pattern image of a region corresponding to the secondary electron image while varying a determine threshold value for the pattern portion including the feature point by using the information.