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Complexity theory is an important application to both natural science and social science. This paper analyzes enterprise information resources integration problem in the vision of complex system. The enterprises, supply chains and integration processes are considered as complex systems. Model is built with agent-based modeling method, and simulations are set on RePast platform. Enterprises' behavior characters in the integration process are analyzed based on simulation results. It's a fresh explore of Complex Adaptive System (CAS) theory in economics.