Abstract: To solve the issue of un-stable operation of thermal power units caused by severe fluctuations in the power grid, a secondary frequency regulation control strategy assisted by flywheel energy storage considering the operation stability of thermal power plant was proposed. Firstly, a secondary frequency regulation control model for ultra-supercritical thermal power units integrated with the flywheel energy storage was developed. Then, a non-linear decomposition method for AGC instructions based on constraints of multi-layer variable gain rates was proposed. Finally, a fitness function was designed based on the unit stability and the AGC performance of the system, and the whale optimization algorithm (WOA) was used to obtain the optimal parameters of limiting algorithm. Based on the above method, a collaborative control strategy of secondary frequency regulation was designed for the integrated system of thermal power unit and energy storage. A simulation verification was conducted on the integrated system with a 1 000 MW thermal power unit and flywheel energy storage as an example. The results show that the proposed control strategy can effectively respond to high-frequency commands of the integrated system without affecting the frequency regulation performance, reduce the action amplitude of thermal power unit, and improve the stability of power unit operation.