In view of the increasingly prominent contradiction between supply and demand of water resources in the Shaying River Basin, according to the actual situation of the Shaying River, the principle and process of the water resources allocation in the Shaying River Basin are proposed, and the water resources allocation model is established based on MIKE BASIN software. The model is applied to water resources allocation in Henan section of the Shaying River Basin from 2015 to 2016. The calculation results show that under the ecological flow guarantee rate of 100%, except the upstream area of the Zhongmo control section, there are different degrees of water shortage in the ranges between other control sections before water resources allocation; according to the results of water resources allocation with the model, the scheme of water transfer from the Yinghe River and other rivers and reservoirs to Zhengzhou City, Kaifeng City, and other water-deficient cities can reduce the degree of water shortage in Henan section of the Shaying River Basin, demonstrating that the model is effective for water resources allocation.