Composite energy storage device is the future development direction of energy storage in stabilizing the wind power fluctuations. This paper takes composite super capacitor and different battery media for example and studies the optimal configuration method of energy storage capacity. Considering the nonstationarity of the wind power, the task of stabilization using Empirical Mode Decomposition (EMD) is split. Then, complementary stabilization is used to realize the energy storage of mutual advantage complement and improve the smooth degree. At last, considering economics, smooth and battery life, the model of capacity determination of hybrid energy storage is built. In this model, cost efficiency is the objective function and rain flow counting method is used to calculate the loss of battery life. This model analyzes whether it can improve the economic efficiency and smooth capacity of the scheme or not if allowing to overcharge and over discharge appropriately. It is verified that under reasonable cooperation scheme composite different battery media can increase the stabilizing ability of unit investment compared to the single battery medium.