An ion source apparatus includes a rare gas supply source supplying rare gas instead of ion source gas to a plasma chamber, means to determine time and timing for cleaning electrodes in consideration of a collecting amount of insulation layers accreting to the electrodes of an extraction electrode system. Based on the above, the ion source apparatus removes the insulation layers by sputtering with ion beam of the rare gas while adjusting extraction or accelerate voltage and supply amount of the rare gas as a setting parameter. Moreover, by adjusting the setting parameter which changes a diameter of ion beam based on the rare gas when the ion beam collides onto each electrode surface of the extraction electrode system, the beam diameter is focused within an effective range in which intension of the sputtering of the insulation layers is maximized thus evenly removing the insulation layers.