An electron beam apparatus includes a movable table which mounts a specimen, an electron optical system including an electron beam source which emits electron beams, an element for deflecting the emitted electron beams, an objective lens for converging and irradiating the deflected electron beams onto the specimen mounted on the table, and a detector for detecting a secondary electron emanated from the specimen by the irradiation of the electron beams. A surface height detection unit is provided which optically detects a height of a surface of the specimen by projecting light onto the surface of the specimen from an oblique direction to the surface and detecting light reflected from the specimen. A focus controller is provided for focusing the electron beam onto the surface of the specimen by controlling a position of the table in a height direction in accordance with the height information from the surface height detection unit.