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Water resources system has obvious complexity and uncertainty, so water resources allocation and scheduling management is a typical group decision-making problem. Determining how to generate the optimum solution set by computing is the key to the research and development of water resources scheduling decision group support system. For this problem, in the existing group decision support systems on water resources scheduling, the effective methods have not been developed. This paper proposes the algorithm of group decision making optimal scheme set based on Agent calculation. The proposed algorithm can generate the optimal scheme set by using the multi-Agent calculation based on the genetic algorithm. Simulation results show that the proposed algorithm can make the coordination satisfaction degree of each group decision-making convergence, and effectively generate optimal solutions set through calculation.