An electron beam apparatus including an electron gun for directing a plurality of primary electron beams onto a sample, an objective lens for forming an electric field to accelerate a plurality of secondary electron beams emitted from the sample, and a separator for separating the plurality of secondary electron beams from a primary optical system and for directing the plurality of secondary electron beams into a secondary optical system for guiding to a detector outputting a detection signal of the secondary electron beams. A deflector deflects the secondary electron beams in the secondary optical system. The deflector is controlled to deflect the plurality of secondary electron beams synchronously with scanning of the plurality of primary electron beams, thereby preventing the plurality of secondary electron beams from moving on the detector in response to the scanning of the plurality of primary electron beams.