An electron beam control method has the following steps, selecting one of a plurality of pattern openings by a character beam electrode having a plurality of electrode units to allow an electron beam to pass through any pattern opening on an aperture mask on which the plurality of pattern openings are formed, determining whether or not a synchronization error of deflected operation of the electron beam performed by the plurality of electrode units is equal to or less than a tolerance, determining whether or not the electron beam is irradiated with a sample by selecting the pattern openings in sequence by the character beam electrode in a state of controlling a path of the electron beam by a blanking electrode not to irradiate the sample with the electron beam, when determined that the synchronization error is equal to or less than the tolerance, and decreasing the tolerance when determined that the electron beam is irradiated with the sample.