A particle beam therapy system comprising a treatment table, a treatment table control unit and an irradiation control unit configured to output an instruction for controlling the treatment table control unit, an accelerator and a scanning electromagnet, wherein after the treatment table control unit controls the treatment table so as for a patient isocenter which is reference position of an affected area of a patient to move to a position of an irradiation isocenter which is set at a position which is closer to an irradiation nozzle than an equipment isocenter which is reference of positional relation of the irradiation nozzle and the treatment table, the irradiation control unit outputs an instruction for irradiating the patient with a particle beam.