Abstract: As one of the important flexibility regulation resources, an energy storage system (ESS) occupies an important position in improving the power supply reliability of the power system and participating in auxiliary services. This paper firstly analyzes the mechanism of ESS participation in the electricity spot market. It clarifies the organizational form and pricing logic of ESS participation in the electric energy market and the frequency regulation market. Secondly, it considers the operating costs of conventional units and ESS, constructs the electric energy market pre-clearance model, calculates the opportunity cost of frequency regulation resources based on the results of the pre-clearance of the electric energy market, and constructs the boundary of the declaration of the dynamic frequency regulation capacity by taking into consideration of the state of charge (SOC) of multiple types of ESS. Then, with the optimization objective of minimizing the total cost of frequency regulation, the frequency regulation market clearing model is constructed, and the real-time generation plan of the electric energy market is generated after deducting the finalized frequency regulation capacity of the unit. Finally, the effectiveness of the proposed joint clearing mechanism is verified through an arithmetic example, and the results show that the proposed method can reduce the joint clearing cost of the market by about 17, 000 yuan, stimulate the participation of energy storage resources in grid regulation, and promote the optimal allocation of resources.