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The manufacturing system transform from hierarchy to parallel, from centralization to distribution which put forward new requirement for production management and control. Holonic Manufacturing System is the new paradigm to organize the production unit. In this paper, the problem of how to demarcate the unit of the manufacturing system, management style of the unit, control structure and the corresponding control method are presented. Order settlement in manufacturing system reconfiguration model is put forward, order intelligent operation series is guided by Differential Evolution (DE) algorithm, Simulation results show that the proposed model and algorithm are effective to order evaluation and implementation .