Abstract: With the commercialization of energy storage technology and the promotion of hybrid energy storage, large-scale energy storage systems are increasingly exhibiting significant heterogeneous characteristics. The differences in physical characteristics across different energy storage units increase complexity of energy management and power allocation within the power system. Therefore, we conduct research on the optimization operation strategy of microgrids incorporating heterogeneous hybrid energy storage units. Firstly, for a microgrid system, a mathematical model for microgrid optimization scheduling with heterogeneous hybrid energy storage units is established. The objective of this model is to maximize new energy consumption, minimize the purchase of electricity from the superior grid, and minimize the load loss on the user side. Secondly, for heterogeneous energy storage units, considering the disparities in power, capacity, and initial SOC of heterogeneous hybrid energy storage units, a clustering method for heterogeneous energy storage units and a charging and discharging sorting strategy are proposed. Subsequently, a dual layer scheduling strategy for microgrid systems with heterogeneous energy storage units is developed with the power response characteristics of hybrid energy storage clusters taken into account. Finally, a microgrid system containing heterogeneous hybrid energy storage units is utilized as a case study to validate the method proposed in this paper. The results demonstrate that this method effectively reduces computational complexity while achieving optimized coordination and cooperation among hybrid energy storage units.