In an electron beam exposure system controlled by a computer, the system includes: an electron optical device for generating electron beams and irradiating the beams to a sample on a stage through a plurality of electron lens, a main deflection coil, and sub deflection electrodes, to form predetermined circuit patterns on the sample. The system also includes a position control device controlling the driving of the stage based on a stage position coordinate designated by the computer, detecting an actual stage position coordinate, and calculating an error value between the designated stage position coordinate and the actual stage position coordinate, the error value being divided into two components of an upper bits portion having an relatively large error value and a lower bits portion having a relatively small error value, and a deflection control device controlling the direction of the electron beams based on the main pattern data corrected by the upper bits portion and the sub pattern data corrected by the lower bits portion, and based on selected main and sub wait times determined by exposure and non-exposure timings.