An electron beam apparatus equipped with a height detection system includes an electron beam unit emitting an electron beam to the specimen, and a height detection system for detecting height of the specimen which is set on a table. The height detection system includes an illumination system configured to direct first and second beams of light through a mask with a multi-slit pattern to a surface of the specimen at substantially opposite azimuth angles and at substantially equal angles of incidence, first and second detectors which respectively detect first and second multi-slit images of the first and second beams reflected from the specimen and generate output signals thereof, and a device which receives the output signals and generates a comparison signal which is responsive to the height of the specimen. An objective lens of the electron beam unit is controlled in accordance with the comparison signal.