Logistics system is a complex socio-economic system, and its core is the whole enterprise logistics integration, which includes the integration of the basic processes and objects, information integration of the supply chain, and the business integration of logistics business. In this paper the supply chain management is regarded as a breakthrough point, and on the basis of the research on current supply chain simulation, Agent-based supply chain simulation is introduced. In this paper, the Agent-based supply chain simulation modeling and realizing method is systematically researched. And the experimental results show that the simulation method is effective and advanced, and it is very effective to solve many problems of supply chain and achieve supply chain optimization, which can generate huge economic benefits for the businesses and the community.