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One of the features of agile supply chains is their organic combination of batch production mode and customization production mode. Aimed at this feature, components and parts of products can be divided into general parts which are made according to batch production and diversity parts according to customization production. And different inventory control strategies can be adopted corresponding to these two kinds of production modes. Moreover, the production activities of general parts present comparatively stronger continuity, and the production activities of diversity parts and the distributing and transporting of both kinds of parts present some discreteness. Therefore agile supply chain systems can be considered as dynamic systems mixed with continuous variables and discrete ones. Based on above consideration, hybrid Petri net is used to model and simulate an agile supply chain hybrid dynamic system. The results of the simulation indicate that hybrid Petri net can effectively describe the dynamic characteristics of agile supply chain systems.