The invention relates to an energy route-based layered synergic control method and system of a microgrid. The energy route-based layered synergic control method comprises the steps of acquiring a DC bus voltage currently accessed to an energy route and a working state of a current energy route; and performing layered synergic control on the microgrid by the energy route according to the DC bus voltage currently accessed to the energy route and the working state of the current energy route. Synergic control is performed on an energy storage battery and a regenerative energy system which are connected to the energy route according to the DC bus voltage accessed to the energy route and the working state of the energy route, the stability of the microgrid system is improved, an SOC state of the energy storage battery is monitored by an energy synergic controller, the working state of the energy route is controlled, automatic adjustment of an SOC value of the energy storage battery is achieved, and the capability of handling an abrupt fault of the energy route is improved.