An ion generator includes an ion source control unit that controls a gas supply unit and a plasma excitation source in accordance with a current ion source condition and a new ion source condition to be employed subsequent to the current ion source condition, a retention time obtaining unit that obtains retention time for the current ion source condition, and a pre-treatment condition setting unit that sets a pre-treatment condition defining a pre-treatment for forming a surface layer region suitable for the new ion source condition on a plasma chamber inner wall based on the current ion source condition, the retention time, and the new ion source condition. The ion source control unit is configured to control the gas supply unit and the plasma excitation source in accordance with the pre-treatment condition when the current ion source condition is changed to the new ion source condition.