The invention discloses a wind power and photovoltaic microgrid water pumping and energy storing power generation system. The system comprises a microgrid direct-current bus, an alternating-current bus, a system controller, a photovoltaic power generation subsystem, a DC-DC controller, a capacitor switch set, a super-capacitor set, an energy-storing battery set, a two-way DC-DC controller, a wind power generation subsystem, an AC-DC controller, a DC-AC controller, a water pump switch set, a water pump unit, a selector switch set, a reversible water turbine set, a thrown-in switch set, a power generator set, a water turbine set, a booster station and a large power grid. The wind power generation subsystem and the photovoltaic power generation subsystem can be subjected to running control at maximum power, maximum energy acquisition is guaranteed, system power balance and electric energy quality are not considered, the thrown-in set number of the super-capacitor set is controlled, smoothing is performed on the voltage of the microgrid direct-current bus, and the bus voltage is kept stable. The electric energy quality problem caused by wind power and photovoltaics can be neglected, the power generation utilizing rate of renewable energy is increased, and reliable, controllable and stable electric energy is provided for the large power grid.