An electron microscope includes an illuminating lens system that illuminates an electron beam that is emitted from an electron source onto a specimen as a planar illuminating electron beam having a two-dimensional spread, an imaging lens system that projects and magnifies the reflecting electron beam emitted from the specimen to project and form a specimen image, a beam separator that separates the illuminating electron beam from the reflecting electron beam, and a controller. The controller controls the reflecting electron beam so as to go straight through the beam separator, and the illuminating electron beam so as to keep a deflection angle of the illuminating electron beam which is made by the beam separator substantially constant.