The present invention provides a high frequency switching method and system of a power system. The method comprises the steps of calculating a switching amount upper limit of each round of high frequency switching of the power system, and determining a switching amount of each round of high frequency switching according to the switching amount upper limit. Compared with the prior art, the high frequency switching method and system of the power system can prevent the system frequency from over reducing due to switching off too many generators, so that a low frequency load shedding apparatus of the power system does not misoperate, and load loss is prevented.