High temperature superconducting magnetic energy storage (HTS SMES) is known as an effective solution to significantly decrease the voltage and power fluctuations of grid connected wind power generation system (WPGS). This paper implements an effective control scheme of a back-toback converter with shunt-connected HTS SMES for the frequency regulation of an islanded microgrid. The back-to-back converter is used to connect the WPGS to the grid. A large-scale HTS SMES is linked to the DC side of the back-to-back converter through a two-quadrant DC/DC chopper. An adaptive control strategy is implemented for the back-to-back converter and the two-quadrant DC/DC chopper to improve the efficiency of the whole system. The performance of the proposed control system was evaluated in a test power system using PSCAD/EMTDC. The simulation results clearly show that the back-to-back converter with shunt-connected HTS SMES operates effectively with the proposed control strategy for stabilizing the power system frequency fluctuations.