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Wind power fluctuations that have adverse impacts on power quality are becoming more serious as wind energy reaches higher level of penetration. This paper focuses on the control design of super-capacitor energy storage system (SCES) which serves for the whole wind farm. The control method of the aggregated SCES is proposed for smoothing medium frequency wind power fluctuations and maintaining wind farm terminal voltage. A modified SCES controller is studied including active and reactive power decoupled control, double-loop control of bidirectional buck-boost converter and super-capacitor voltage management. Design of the control loops are discussed based on the SCES small-signal model. The effectiveness of the control strategy is validated by simulation in PSCAD/EMTDC.