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This paper proposes a research method for mitigating wind power fluctuations in a hybrid energy storage system considering the confidence level of wind power volatility. First, the typical daily wind power output is subjected to Fourier spectrum analysis to determine the frequency range of wind power output, and combined with low-pass filtering to find the optimal cutoff frequency, for obtaining energy storage reference power; Then determining the optimal energy storage reference power by comparing the energy storage reference powers solved at different confidence levels. Finally, empirical mode decomposition (EMD) is used to decompose the stored energy into a series of intrinsic mode functions(IMFs), demarcation of the energy storage reference power with minimum aliasing in the instantaneous frequency-time curve, the high frequency part is configured by power type energy storage, and the low frequency part is configured by energy type energy storage. The simulation of the wind farms in a certain area of Hunan Province is carried out. The result shows that proper reduction of confidence level can reduce energy storage power and capacity.