Abstract: Aiming at how to reduce the frequency modulation loss of thermal power units, to improve the frequency modulation performance of the system, and to reduce the life cycle cost of energy storage, we propose a dual-level optimal configuration model of hybrid energy storage assisted thermal power units participating in automatic generation control (AGC). The upper layer model is composed of empirical mode decomposition (EMD) and multi-objective optimization configuration model, in which EMD is based on AGC allocation strategy between thermal power and hybrid energy storage, and the cost-benefit difference in the life cycle and AGC comprehensive evaluation index K_p is taken into account in the multi-objective optimization configuration model. The upper layer model provides AGC preliminary decomposition instructions and power and capacity constraints for the underlying model. The underlying model consists of a hybrid energy storage control strategy considering state of charge (SOC) recovery and a thermal power-hybrid energy storage frequency modulation response model. The AGC firstly decomposed by EMD is reassigned to each frequency modulation resource, and the output curve and SOC curve are provided to the upper model. Then, a multi-objective particle swarm optimization algorithm based on technique for order preference by similarity to an ideal solution (TOPSIS) was used to solve the two-layer model, which avoids the contingency of the traditional multi-objective particle swarm optimization algorithm to determine the global optimum in the Pareto solution set. Lastly, the simulation analysis of operation data of a power plant in North China is performed. The results show that the hybrid energy storage dual-layer optimization model can effectively reduce the frequency modulation loss of thermal power units and significantly improve the economy of the combined thermal-storage frequency modulation system. The conclusion can provide a reference for the configuration scheme of hybrid energy storage auxiliary traditional frequency modulation power supply in the future.