In this study, a cooperative control based on real-time empirical modal decomposition(EMD) is proposed for a hybrid energy storage system(HESS) consisting of energy-based and power-based storage to smooth out the power fluctuations of distributed generations(DGs). Firstly, the unbalanced power is decomposed using real-time EMD, and the reference power of each energy storage is determined by superimposing the intrinsic modal function(IMF) to achieve short time-scale coordinated control; secondly, the reference power of each energy storage power is modified based on fuzzy control and storage of charge (SOC) to achieve long time-scale coordination; Finally, the simulation results are analyzed to show the effectiveness of the proposed strategy. The proposed strategy is effective in reducing the number of times the energy storage element is operated and extending the service life, and obtain a better effect of Photovoltaic(PV) fluctuation smoothing.