Abstract: The invention provides an ion generation system, including a high voltage pulse generator, an ion balance detector and a controller. The controller is configured to receive a signal from the ion balance detector and send a regulation signal to the high voltage pulse generator to regulate the balance of positive/negative ions of the ion generation system. The invention also provides a method for controlling the ion balance where the ion generation system is utilized. By controlling the width difference between the positive peak pulse and the negative peak pulse of a high voltage pulse or regulating the peak difference between the positive peak and the negative peak of an output pulse high voltage, the yield of positive and negative is controlled, thus balanced ions output-is achieved.