The "14th Five-Year Plan" emphasizes that the energy structure in China will change in the future. In order to reduce carbon emissions, the installed capacity of new energy such as wind power and photovoltaics will usher in a substantial increase, and the demand for frequency modulation (FM) of the system will further increase. The pricing and clearing mechanism of the FM auxiliary service market has a significant impact on grid dispatch and safe operation. A reasonable FM market design and pricing mechanism is conducive to promoting the optimal allocation of FM resources and reducing carbon emission. Considering that energy storage resources have good frequency modulation performance, this paper mainly discusses the frequency modulation auxiliary service mechanism of different energy storage permeability under the joint clearing mode. The price mechanism of the frequency modulation market with the energy storage permeability factor is proposed. Taking the existing FM auxiliary service market as a reference, a method for calculating FM performance indicators based on the analytic hierarchy process (APH) is proposed. A joint clearing model of the main energy and FM auxiliary service market is given, a case simulation is performed, and a comparative analysis with the traditional clearing model is performed to verify the effectiveness of the proposed method.