The invention discloses a balance switching method for storage battery sets in a hybrid energy storage system. The balance switching method includes the steps that the charge state of a super capacitor and the charge states of all the storage battery sets in the hybrid energy storage system are monitored, and according to the different charge states of the super capacitor, the storage battery sets are selectively switched. According to the balance switching method for the storage battery sets, the charge state of the super capacitor in the smoothing process of the wind power is adjusted, the charge state of the super capacitor is kept the optimal state accordingly, and adjusting capacity is high; meanwhile, the charge states of all the storage battery sets in the charging process and the discharging process can be balanced, the discharge depth of the storage battery sets is reduced, and therefore the cycling life of the storage battery sets is prolonged. By means of the balance switching method, the high power density of the super capacitor and the high energy density of the storage battery sets can be effectively combined, and the redundancy rate of a device is decreased, fluctuation of a wind power plant is improved, and the high-performance hybrid energy storage system is formed.