An ion implantation apparatus includes a beam scanner that provides a reciprocating beam scan in a beam scan direction in accordance with a scan waveform, a mechanical scanner that causes a wafer to reciprocate in a mechanical scan direction, and a control device that controls the beam scanner and the mechanical scanner to realize a target two-dimensional dose amount distribution on a surface of the wafer. The control device includes a scan frequency adjusting unit that determines a frequency of the scan waveform in accordance with the target two-dimensional dose amount distribution, and a beam scanner driving unit that drives the beam scanner by using the scan waveform having the frequency determined by the scan frequency adjusting unit.