With the large-scale integration of wind power and other renewable energy sources, the frequency regulation capacity and effect of traditional frequency regulation power sources are difficult to meet the requirements of power grid. To solve this problem, a comprehensive control strategy based on the frequency regulation signal optimization of a battery energy storage system which assists the thermal power unit to participate in secondary frequency regulation is proposed. First, a simulation model of energy storage that meets the power grid’s frequency regulation requirements is established. Based on this model, the allocation mode of area control error signal and area frequency regulation requirement signal is analyzed in the complex frequency domain, and the switching criterion for frequency regulation signal is determined by combining the advantages of the two control signals. Then, considering the economy and efficiency of energy storage frequency regulation, the allocation coefficient is optimized by a decomposed multi-objective evolutionary algorithm to reduce the frequency offset and optimize the cost of frequency regulation. Finally, the effectiveness of frequency regulation signal switching criterion and multi-objective evolutionary algorithm in optimizing the energy storage allocation coefficient is verified by step disturbance simulation. The comprehensive control strategy is verified by continuous disturbance simulation, and results show that it can not only reduce the system frequency offset effectively, but also lower the operating cost of energy storage.