First ions and second ions that are heavier than first ions are generated in an ion source. One kind of ions of the first ions and second ions is injected into an accelerator by action of a switching magnet and accelerated in the accelerator. An ion beam including the one kind of ions is extracted from the accelerator to a beam transport system and a tumor volume of a patient is irradiated with the ion beam from an irradiation nozzle. In the irradiation of the ion beam, a tumor volume depth and the largest underwater range of each ion species are compared, and an ion species in which the tumor volume depth becomes the longest underwater range or lower is injected into the accelerator, and accelerated by the accelerator. The tumor volume is irradiated with the ion species.