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China faces a very serious situation of water resources, with increasingly conspicuous problems of water resources shortage, serious water pollution, deterioration of the water ecological environment, and so on, which have become major bottlenecks inhibiting sustainable economic and social development in the country. Applying the strictest water resources control system is the most effective way to solve these water resources problems. The optimal water resources allocation is the core issue of the strictest water resources control system. The challenges and controversies in optimal water resources allocation research under the strictest water resources control system have been analyzed according to the relationship between the strictest water resources control and the optimal water resources allocation. In order to satisfy the requirements of the strictest water resources control system, the dynamic structure of new water resources allocation model, the optimal solution algorithms and the scheme evaluation methods have been presented and suggested. What have been analyzed and suggested in this paper will be very helpful for applying the strictest water resources control system in China.