A cryopump includes a refrigerator which cools a cryopanel and a controller which receives a control signal representing an operation mode from a beam irradiating apparatus and controls the refrigerator based on the control signal. The operation mode includes an irradiation mode for irradiating a beam to a target and an idle mode for diverting the beam from the target or keeping the beam with a level weaker than that of the irradiation mode. The controller controls the refrigerator such that the cryopanel is cooled in both the irradiation mode and the idle mode to a cooling temperature at which gas molecules are held and allows the cooling temperature in at least a part of the period of the idle mode to be higher than that of the irradiation mode.