The invention discloses a hybrid energy storage control system for stabilizing wind power fluctuation and a control method. The system comprises a power smooth acquisition unit and a hybrid energy storage coordination control unit. Wind power set power can be acquired by the power smooth acquisition unit in real time, the wind power set power is contrasted with a desired output power value of a wind power set, after amplitude limit processing, the wind power set power is sent to the hybrid energy storage coordination control unit, Karman adaptive low pass filtering is carried out by the hybrid energy storage coordination control unit according to a power deviation value to acquire a power output value of a wind power set, a first fuzzy controller is for adjusting time constant of a Karman low pass filter, correction on a power output value of the hybrid energy storage system is carried out by a second fuzzy controller after output power of the Karman low pass filter and energy storage cell state-of-charge SOC are acquired by the second fuzzy controller, after the amplitude limit stage, optimum power output is acquired by an energy storage cell and a super capacitor, so over-discharging and over-charging of the cell are avoided, and thereby safety operation of the energy storage system and the optimum wind power fluctuation stabilizing effect are realized.