Abstract: The integration of flywheel energy storage systems (FESS) with thermal power plants offers a promising solution to enhance the frequency stability and security of power grids. An efficient energy management system (EMS) for this integrated setup can significantly improve system regulation performance. Given the unique characteristics of modern, independently structured control systems for thermal and flywheel coupling, as well as the considerable variations in the individual states of flywheel array components, this paper proposes a cooperative control method specifically designed for primary frequency regulation in power systems, taking into account the distinct features of flywheels. The research introduces a double-layer autonomous control technology of flywheel array for flywheel arrays operating within diverse operational modes, optimizing the management of power output and energy storage within the array. The proposed EMS exhibits the capability to comprehensively optimize control parameters for the coupling system in the context of primary frequency regulation. Simulation and field practical application results verify the effectiveness of the proposed control strategy. Compared with the virtual droop control, the system frequency deviation is remarkably reduced by 20.34%, fluctuations of power output and main steam pressure of the thermal power unit are significantly reduced, respectively. Moreover, it augments the flywheel array's ability to track power requirements accurately.