An ion irradiation apparatus is provided. The ion irradiation apparatus includes a support member, a measuring device, and a control device. The support member is larger than the substrate. The measuring device is disposed forwardly in a traveling direction of an ion beam. The ion irradiation apparatus operates in a first mode during which the measuring device is irradiated with a remaining part of the ion beam after being partially shielded by the support member, when the substrate is not irradiated with the ion beam after crossing the ion beam; and a second mode during which the measuring device is irradiated with the ion beam without being shielded by the support member, when the substrate is not irradiated with the ion beam after crossing the ion beam. The control device controls the substrate so that the ion treatment process is performed in the first mode at least one time during the treatment.