Abstract: With the development of large-scale distributed energy resources, microgrid systems—which integrate multiple types of distributed energy resources to form a microgrid—are widely used. However, it is difficult to guarantee the flexible regulation capability of massive microgrids. In this context, this study first considers the allocation of shared energy storage among multiple microgrids and proposes an operational model for the microgrids-shared energy storage system. Second, an interval method is employed to characterize the flexibility demand of the system and quantify the flexibility supply capacity according to the characteristics of individual unit. Subsequently, a two-tier optimization model for multiple microgrids-shared energy storage is proposed, which accounts for the ladder carbon trading and flexibility. Finally, the case study demonstrates that the shared energy storage reduces the total system costs by approximately 15.58% and provides greater flexibility capacity to the system. Additionally, the carbon emissions in the traditional carbon trading model are 9.41% higher than those in the ladder carbon trading model. The proposed allocation method can improve the security and stability of multiple microgrids, as well as promote the flexibility, economy, and low-carbon performance of the multi-microgrid-shared energy storage system.