Researchers usually use hybrid storage system which consists of super-capacity and battery to smooth fluctuating power in order to avoid the battery charging and discharging frequently. This paper puts the point on how to reduce the depth of discharge of the battery further, and proposes a fuzzy control strategy which based on hybrid storage system, and then verifies the proposed strategy by PSCAD. Simulation results indicate that the proposed strategy can make the hybrid storage system distribute compensation power reasonably between different storage units, and prolong the life of battery by reducing the depth of discharge effectively. The proposed strategy also can improve the energy ratio of super-capacity and the performance of the whole hybrid storage system.