An electron beam lithography system 10 comprises an electron gun including a rectangular cathode 1 having an emission surface having an aspect ratio of other than 1, an illumination optical system 3 of an asymmetric lens system including multipole lenses Qa1 and Qa2, a CP aperture 5, and a projection optical system 8 of a symmetric lens system including multipole lenses Qb1 through Qb4. This electron beam lithography system 10 is used for emitting an electron beam at a low acceleration of 5 kV or less from the rectangular cathode 1, for controlling the illumination optical system so as to form an image of a desired character of the CP aperture 5 on an isotropic plane of incidence at different demagnifications in minor-axis and major-axis directions in accordance with the aspect ratio of the rectangular cathode 1, and for controlling the projection optical system 8 so that the electron beam leaving the CP aperture 5 as an aperture image is incident on a substrate 21 at the same demagnification in the minor-axis and major-axis directions and at different incident angles in the minor-axis and major-axis directions while passing through the trajectory without establishing any crossovers.