The invention discloses a control method and system of an AC-DC hybrid microgrid. The method comprises the following steps of receiving a first instruction for converting a preset running mode from a current running mode; calling a switching mechanism corresponding to the first instruction according to the first instruction; switching the current running mode into the preset running mode according to the switching mechanism. The control method is suitable for the AC-DC hybrid microgrid which the capacity of a DC-side main power generation device is smaller than the capacity of an AC-side main power generation device, smooth switching of all running modes can be achieved, and the safety performance of the AC-DC hybrid microgrid is improved.