A beam extraction process (interruption and restart) is appropriately performed when a failure occurs during irradiation of a spot group so that the irradiation is safely and efficiently performed with high accuracy.A charged particle irradiation system includes a synchrotron 12 and a scanning irradiation unit 15 that has scanning magnets 5A and 5B. The scanning irradiation unit 15 scans an ion beam extracted from the synchrotron 12 over a subject. The extraction of the ion beam from the synchrotron 12 is stopped on the basis of a beam extraction stop command. The scanning magnets 5A and 5B are controlled to change a point (spot) to be irradiated with the ion beam, while the extraction of the ion beam is stopped. The extraction of the ion beam from the synchrotron 12 is restarted after the change of the spot to be irradiated. When a relatively minor failure in which continuous irradiation would be possible occurs during irradiation of a certain spot with the beam, the extraction of the beam is not immediately stopped. The extraction of the beam is stopped at the time of completion of irradiation of all spots that belong to a predefined spot group that includes the certain spot without immediately stopping the extraction of the beam.
