The invention discloses a switching system and a switching method of an alternating current filter, relates to the technical field of electric energy quality control, and aims to solve the problem of an alternating current filter switching way in a high-voltage direct current power transmission system that calculation engineering is large, switching form data occupies large storage space and various operation ways of the direct current power transmission system cannot be flexibly corresponded. The switching system of the alternating current filter comprises an aberration rate index judgment device, an alternating current filter selection device and an alternating current filter switching indication device, wherein the aberration rate index judgment device is used for judging whether an initial aberration rate index and a target aberration rate index conform to a standard or not; the alternating current filter switching indication device is used for selecting the alternating current filter which is input into the high-voltage direct current power transmission system in an analog manner; the alternating current filter switching indication device is used for indicating the practical switching operation of the alternating current filter according to the judgment result of the aberration rate index judgment device and the selection result of the alternating current filter selection device. The switching system of the alternating current filter is used for switching the alternating current filter into the high-voltage direct current power transmission system.