The invention discloses a microgrid virtual synchronous generator model prediction control method and a system. The microgrid virtual synchronous generator model prediction control system comprises a virtual synchronous generator and a frequency modulation unit, wherein the virtual synchronous generator mainly has a main circuit and a control system; the main circuit is grid-connected inverter topology and has a renewable energy generation device, a DC/AC converter, an inverter and a filter circuit; the control system is a core for the virtual synchronous generator and comprises a virtual synchronous generator body model and control algorithm; with simulation of mechanical features and electromagnetic features of the virtual synchronous generator, the inverter can have features similar to the synchronous generator; the frequency modulation device is an energy storing device and can absorb or release energy in real time; the energy storage device is accessed to the virtual synchronous generator; and when required power has to be supplemented upon imbalance of the system power, frequency fluctuation can be weakened and system transient power conservation can be guaranteed. System frequency changes can be confined to a safety range by the system, and economic property of the virtual synchronous generator output can be considered at the same time.