In the context of energy structure transformation and power reform, energy storage systems (ESS) play a crucial role in promoting new energy consumption and achieving the “dual carbon” strategic goals. Making their scheduling strategies in multi-scenario applications particularly important. Addressing the issue of imperfect scheduling strategies for ESS as an emerging entity in competitive joint application scenarios, this paper proposes a bi-level optimization model for the joint scheduling of ESS in multi-scenario applications involving electric energy and frequency regulation auxiliary services. The case study results demonstrate that this model can optimize the charge and discharge strategies of ESS in multi-scenario applications, significantly improving the utilization comprehensive operational benefits of the ESS. This validates the effectiveness and rationality of the proposed model.