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Supply chain members of independent enterprises are different from each other in strategies. Conflict in benefits is inevitable. The supply chain management system (SCMS) based on information system usually emphasizes on the function of the information technology. To achieve collaboration management, four main problems must be solved:1)Belief among supply chain members,2)Motivations of supply chain members, 3)Allocation of interests among supply chain members, 4)Integration of supply chain information system.This paper intends to analyze these key problems, and put forward some resolutions.