An ion implantation apparatus comprises an ion beam source for generating an initial ion beam, a bundled ion beam generator adapted to change the initial ion beam into a bundled ion beam based on a predetermined frequency to pass the bundled ion beam for a first time while passing the initial ion beam for a second time, a beam line for accelerating the ion beam having passed through the ion beam generator, and an end station for arranging a wafer therein to allow the ion beam accelerated by the beam line to be implanted in the wafer, the end station operating to move the wafer in a direction perpendicular to an ion beam implantation direction, so as to implant the bundled ion beam in a first region of the wafer and the initial ion beam in a second region of the wafer.