Energy storage device plays an irreplaceable role in micro-grid and has a great market application prospect in micro-grid. This paper considers the reliability of wind turbines and photovoltaic units when configuring energy storage capacity and adopts the sequential Monte Carlo method to simulate the normal operation and outage probability of wind turbines and photovoltaic units. In view of the complementary advantages of battery storage and super-capacitor storage, discrete Fourier transform (DFT) is used for the spectral analysis of unbalanced power during a period. The optimization model with the goal of minimizing comprehensive cost is established in the planning cycle, and the optimal capacity for hybrid energy storage is determined. The calculation example analysis shows that when considering the reliability of wind turbines and photovoltaic units, the rated capacity of hybrid energy storage configuration is greater than the result of not considering the reliability, which provides reference for further research on energy storage planning of micro-grid.