A beam processing system comprises a rotary disk mounted thereon with processing objects, a controller for controlling a reciprocating drive mechanism, and a beam width measuring unit for measuring a beam width of a processing beam. The controller sets an inner and an outer overscan position depending on a measured value of the beam width. The controller, based on the number of rotation of the rotary disk per unit time, a scan speed and the number of reciprocating scan times, a reversal start timing of the rotary disk at at least one of the inner and the outer overscan positions, and the measured value, controls the reciprocating drive mechanism so as to ensure an overlap region between a last and a current processing beam irradiation region on each of the processing objects, the overlap region overlapping at least half of the last processing beam irradiation region.