With the increasing penetration rate of power generation from a high proportion of renewable resources, energy storage plays an increasingly important role in the process of stabilizing uncertainty and volatility in the new power system. In order to encourage them to better participate in the operation of the power grid, it is necessary to pay more attention to the applicability of the market mechanism to energy storage market entities when allocating energy storage resources in a market-oriented manner. Considering that the existing mechanism fails to precisely reflect the technical characteristics of energy storage and the operating costs when participating in different types of markets, this paper proposes a joint clearing model of electric energy and frequency modulation auxiliary service market based on that energy storage participates in the market in a flexible energy operating state. To describe the energy loss of energy storage in the process of frequency modulation, the new model introduces the frequency modulation energy loss coefficient to further model the energy coupling relationship between these two different markets. Finally, the effectiveness of the model in reflecting the operation characteristics of energy storage is verified by simulation comparison.