For man-machine cooperation effectively applying to warehousing system, on the basis of defining the concept and classification of man-machine cooperation, the new model of man-machine cooperation is put forward, in which each function module is an agent. In order to describe the model more clearly and analyze the relationship and internal data processing of Agents, Petri net is used, which forms the Petri net detailed model of man-machine cooperation in warehousing system based on agent. Its key technology is analyzed. The software platform of man-machine cooperation in the system is realized based on the model previously established, using Java and VC++ 6.0 as the programming tools, Access as background database, and Jade as the running platform of Agent. Thus the warehousing simulation system of man-machine cooperation is established and assisting AGV to get rid of the dead interval of path of man-machine cooperation are realized in warehousing system. It lays the foundation for further practical human-machine cooperation of warehousing system.