Energy coordination is an important requirement for stable operation of the multi-microgrid system. This paper presents a hierarchical control scheme based on multi-agent system (MAS) to cope with the problem of energy coordination of a multi-microgrid system. Based on java agent development framework (JADE), a layered multi-agent system framework is constructed, including distributed generation level, microgrid level, multi-microgrids level and distribution network level. The energy coordination process and optimization objectives are discussed. Depending on the properties of the agents’ autonomy and collaboration, the system could ensure the energy coordination in a microgrid and among microgrids. An example of a typical multi-microgrid system is used to discuss the function of the agents and their interactions. The results verify the effectiveness of the hierarchical control scheme based on multi-agent system and its applicability for hierarchical energy management of multi-microgrid system.