—This article presents an enhanced control strategy for a direct-driven permanent synchronous generator based wind-power generation system with a flywheel energy storage unit. The behaviors of the direct-driven permanent magnet synchronous generator system with a flywheel energy storage unit under unbalanced grid fault conditions are investigated. Three control targets for the grid-side converter during network unbalance conditions are identified, including eliminating the oscillations in the total active power or reactive power or no negative-sequence current injecting into the grid. Meanwhile, the DC-link voltage oscillations can be effectively suppressed during the unbalanced grid fault by controlling the flywheel energy storage unit. Furthermore, a proportional–integral-resonant controller is designed for the flywheel motor to eliminate the oscillations in the DC-link voltage. Finally, the proposed coordinated control strategy for the direct-driven permanent magnet synchronous generator system with a flywheel energy storage unit has been validated by the simulation results of a 1-MW direct-driven permanent magnet synchronous generator wind power generation system with a flywheel energy storage unit under unbalanced grid fault.