The invention provides a control method for stabilizing wind and light output power fluctuation through a hybrid energy storage system. The control method is characterized in that a super capacitor and a storage battery complement each other to conduct two-level stabilizing on wind and light output power, the same algorithm is adopted in two levels of stabilizing, required smooth wind and light output power, surplus capacity of an energy storage element and other data are collected and analyzed, an expectation value of the wind and light output power is calculated, and meanwhile the wind and light power fluctuation and the electrical charge state of the energy storage element are considered to conduct optimizing control on a mobile step size; finally, deviation between a wind and light output power actual value and the expectation value serves as the stabilizing target of the energy storage element, charging and discharging of an energy storage unit are controlled, and smoothness of the wind and light output power is achieved. On the basis that the highest power output of wind electricity and photoelectricity can be kept, by flexibly and rapidly controlling the storage battery and the super capacitor, stabilization of the wind and light power fluctuation is achieved, electricity energy quality is effectively improved, and the energy using ratio and admitting ability for renewable energy sources of a power grid are improved.