In order to solve the problem of intermittence and fluctuation of output power of photovoltaic (PV) power generation system, a fuzzy control based optimization method for power distribution of hybrid energy storage system is proposed. Compared with the traditional hybrid energy storage system (HESS) control method, this method can use the ensemble empirical mode decomposition (EEMD) and fuzzy control algorithm to realize the reasonable distribution of charge and discharge power of hybrid energy storage system. EEMD technology is used to decompose the unbalanced power signal in the system, and realize the power distribution of super capacitor and battery according to the characteristics of energy storage system. The fuzzy controller is used to optimize the distribution power of the hybrid energy storage system, to control the charge and discharge of the energy storage device reasonably. Under the action of the fuzzy controller, the hybrid energy storage system can choose the appropriate operation mode to maintain the stability of DC bus voltage according to the energy storage state of charge (SOC) and power fluctuation. Finally, the simulation example verifies the rationality and superiority of the proposed method.