Supply chain simulation is a fundamental approach for supply chain prediction, management, evaluation, and improvement. In order to simulate member behavior, organizational strategy, and management strategy of the supply chain, an agent-based modeling and simulation approach on multi-stage supply chain operation was proposed in this paper. First, the model structure of multi-stage supply chain operation was introduced. Then, the individual agent behavior model was emphatically studied, and hierarchical colored Petri-nets were used to describe the agent behavior process and cooperative behavior process. Finally, the model was validated using a series of simulation which focused on the agent inventory strategy.