From ecological security to ecological priority, it is the requirement of the times for high-quality economic development to allocate water resources in the river basin. From the perspective of ecological priority, a multi-agent cooperative allocation model of water resources in the basin was built, in which the multi-attribute index system, the index weight design and the DEA method were integrated to realize the reward and punishment mechanism.The effectiveness of the model was verified by taking the Nansi Lake Basin as an example. The paper aims to achieve the design and model of the reward and punishment mechanism for water resources allocation under ecological priority, through which the local governments would be forced to take the road of high-quality development of “water conservation, economic transformation and ecological protection”.