The invention discloses a method for controlling a hybrid energy storage system based on a fuzzy logic controller. The method mainly comprises a low pass filter, the fuzzy logic controller and a PSO (particle swarm optimization) algorithm, wherein the low pass filter is used for decomposing a power fluctuating signal into a high-frequency signal and a low-frequency signal; the fuzzy logic controller is used for processing the inputted low-frequency signal and an SOC (system on chip) signal of a supercapacitor through a logic relationship so as to obtain a control signal for charging and discharging of the supercapacitor; the PSO algorithm is used for optimizing the parameters of a membership function of the fuzzy logic controller. The method has the advantages that the depth discharging and peak current of a storage battery can be reduced, and the working efficiency of the hybrid energy storage system is improved.