An electron beam inspection apparatus includes a stage to mount a substrate to be inspected thereon and to be continuously movable, an electron beam column, while the stage continuously moves, to scan the substrate by irradiating the substrate with multi-beams composed of a plurality of first electron beams in a plurality of beam rows, in each of which corresponding beams of the plurality of first electron beams are arranged at a same pitch in a straight line, such that the center of each of irradiation regions irradiated with the multi-beams does not overlap with the other irradiation regions in a movement direction of the stage, and a detector to detect a secondary electron emitted from the substrate due to irradiation of the multi-beams on the substrate.