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In the inter-enterprise cooperative manufacturing mode, meeting the dynamic demand of manufacturing information management, comprehensively utilizing and fully communicating, based on holonic theory, this paper describes a practical system framework for holonic design and operations in a distributed manufacturing environment using multi-agent system. Based on the negotiation mechanism of multi-agent, the optimizing of dynamic holonic manufacturing systems is study. A dynamic holonic manufacturing systems implementation is developed to demonstrate and validate the proposed idea. It shows that the proposed system can satisfy the agility, distribution, and robustness requirements.