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With the economic and social development, as well as risk management consciousness improved, the importance of risk evaluation is increasingly recognized in project management. Many projects have the characteristic of large-scale, wide-rang, and at great position in national economy. The need for risk management decision support system is valuable and essential. But risk factors in projects are complex and close association with each other. Normal risk analyzing methods can not manifest this relationship fully. This paper proposes a new risk management decision support system based on bayesian network, and take the east route of south-to-north water transfer project as an example, build a decision support system. The result shows that bayesian network is effective in complex risk analyzing in decision support system of project management. Moreover, it also can be used for real time risk assessment and decision-making in project management.