A charged particle beam system comprising: an ion source (1, 2) adapted to generate a plurality of kinds of ions different in weight from each other; an accelerator adapted to accelerate one kind of injected ions of the plurality of kinds of ions generated in the ion source; a beam transport system adapted to transport an ion beam extracted from the accelerator, the ion beam including one kind of the injected ions; a rotating gantry adapted to set an irradiation direction of each ion beam to an irradiation target; an irradiation nozzle installed in the rotating gantry, the irradiation nozzle adapted to irradiate each ion beam to an irradiation target in the irradiation direction; and a control apparatus, wherein the ion source is an ion source generating first ions and second ions that are heavier than the first ions; and wherein the control apparatus is a control apparatus adapted to execute a first control accelerating a first ion beam including the first ions by controlling frequency of high-frequency voltage applied to a high-frequency acceleration apparatus so that an underwater range of the first ion beam becomes larger than a set underwater range of a second ion beam including the second ions and the first ion beam reaches the irradiation target when water equivalent depth of the irradiation target in the irradiation direction is larger than the set underwater range of the second ion beam, and a second control accelerating the second ion beam by controlling the frequency of the high-frequency voltage applied to the high-frequency acceleration apparatus so that an underwater range of the second ion beam becomes the set underwater range of the second ion beam or smaller than the set underwater range of the second ion beam and the second ion beam reaches the irradiation target when the water equivalent depth of the irradiation target in the irradiation direction of the second ion beam is the set underwater range of the second ion beam or smaller than the set underwater range of the second ion beam, characterized in that the control apparatus is adapted to execute the first control after the end of the second control. an ion source (1, 2) adapted to generate a plurality of kinds of ions different in weight from each other; an accelerator adapted to accelerate one kind of injected ions of the plurality of kinds of ions generated in the ion source; a beam transport system adapted to transport an ion beam extracted from the accelerator, the ion beam including one kind of the injected ions; a rotating gantry adapted to set an irradiation direction of each ion beam to an irradiation target; an irradiation nozzle installed in the rotating gantry, the irradiation nozzle adapted to irradiate each ion beam to an irradiation target in the irradiation direction; and a control apparatus, wherein the ion source is an ion source generating first ions and second ions that are heavier than the first ions; and wherein the control apparatus is a control apparatus adapted to execute a first control accelerating a first ion beam including the first ions by controlling frequency of high-frequency voltage applied to a high-frequency acceleration apparatus so that an underwater range of the first ion beam becomes larger than a set underwater range of a second ion beam including the second ions and the first ion beam reaches the irradiation target when water equivalent depth of the irradiation target in the irradiation direction is larger than the set underwater range of the second ion beam, and a second control accelerating the second ion beam by controlling the frequency of the high-frequency voltage applied to the high-frequency acceleration apparatus so that an underwater range of the second ion beam becomes the set underwater range of the second ion beam or smaller than the set underwater range of the second ion beam and the second ion beam reaches the irradiation target when the water equivalent depth of the irradiation target in the irradiation direction of the second ion beam is the set underwater range of the second ion beam or smaller than the set underwater range of the second ion beam, characterized in that the control apparatus is adapted to execute the first control after the end of the second control.