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The paper proposed a new thought that a multi-agent organization model was designed, which based on cooperative design system network framework and workflow. The system workflow and system architecture were presented. The ant colony optimization (ACO) method which was improved by Bayes was applied to the partner selection. And the principal component analysis (PCA) method was used to evaluate the design method of design tasks. The collaborative process of negotiation mechanism was discussed. According to the theory analysis, software SPSS was used to deal with the sample data. On the basis of the theory a network of collaborative design prototype system was developed which confirms the system is reliability, practicality and efficiency.