An ion implantation apparatus includes an ion irradiation unit. The ion irradiation unit irradiates a plurality of areas of a target substrate with ion beams each of which reaches the substrate at corresponding one incident angle. An incident angle measuring instrument measures the incident angle of each of the ion beams. A controller is provided with information from the incident angle measuring instrument and controls the ion irradiation unit in accordance with the information so that a difference among incident angles is set to within ±0.1°.