The invention discloses a hybrid energy storage system for stabilizing a wind power fluctuation. The hybrid energy storage system aims at solving the problems of complicated structure and working state optimization of an energy storage system in the prior art. The hybrid energy storage system comprises a supercapacitor, a storage battery and a hysteresis comparison controller, wherein the supercapacitor and the storage battery are cascaded; and the hysteresis comparison controller is connected with the supercapacitor and the storage battery, and provided with a first threshold, a second threshold, a third threshold and a fourth threshold which are ascended and correspond to the dump energy of the supercapacitor. Therefore, frequent action, charging and discharging of the storage battery can be effectively avoided; the service life is prolonged; a charge state fluctuation of the supercapacitor is reduced; the whole economy of the hybrid energy storage system is improved; and a working state of the energy storage system is optimized. The hybrid energy storage system is applicable to research, development, design, operation control, electric energy measurement, expense management and the like of a wind power generation system, has the characteristics of simple structure, good stability, environmental protection and reproducibility, and has a high industry-university-research value.