The invention relates to an ion source beam stability control system and method, and the system is characterized in that the system comprises a needle valve, a gas flow meter, a drive motor, a beam diagnosis element, and a control system; the needle valve and the gas flow meter are sequentially arranged on a pipe between a gas outlet of the ion source gas source gas storage tank and a gas inlet ofthe ECR ion source; the needle valve is connected with the output end of the drive motor through a mechanical driving device, the needle valve is used for controlling the air outlet amount of the ionsource air source air storage tank, and the air flow meter is used for collecting the air flow at an air inlet of the ECR ion source; the control system is electrically connected with the gas flow meter, the drive motor and the beam diagnosis element; and the beam diagnosis element is used for measuring the beam intensity of the ECR ion source. The system can be widely applied to the technical field of ion sources.