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The importance and significance of planning of logistics system is analyzed. The logistics system operational diagram is depicted in general perspective. The mufti-agent system model is introduced and applied to design the planning model of logistics system. The parallel simulation technology is used to improve the efficiency. The genetic optimization is adopted to produce the better planning result in automatic mode, which overcomes the manual evaluation fault of system simulation. The software for the planning approach is developed with the support of swarm simulation package. An application case is demonstrated in the fast part.