Due to wind's unsteady and intermittent characteristic, the active power of wind turbine in the optimal wind-energy tracking control strategy fluctuates with the change of wind speed, which influences the power quality of wind turbine, causes fluctuation of grid frequency, and even causes stability problem to the grid. The control strategy of full power back-to-back pulse-width modulation AC-DC-AC converters of direct-driven permanent magnet synchronous generator is analysed. A flywheel energy storage system with the DC-side of converters with no change of converters' current control strategy is proposed. The energy control strategy to the flywheel energy storage system is designed to smooth the active power of wind turbine, in which the smooth power calculation method is presented. A simulation study is done on a 1.3 MW direct-driven permanent magnet synchronous generator based wind turbine. Simulation results show that the presented energy control strategy to the flywheel energy storage system can effectively smooth the active power of wind turbine to improve the power quality.