Abstract: Provided is an optimal allocation method of a complex water resource system based on a “zoning-grading” theory, including the following steps: first, obtaining basic information data of the water resource system, and then generalizing the complex water resource system into different units; second, dividing the entire complex water resource system into zones according to the water supply relationship among reservoirs, pumping stations, rivers, water pipelines, and water plants, and respectively establishing digital matrices of hydraulic relationships of different zones; and finally, constructing and solving a multigrade optimal allocation model of the water resource system according to the types of water supply sources, and determining a reasonable set of optimal allocation solutions. The present application can simplify the complex water resource system and provide a new way to utilize water resources efficiently.