Abstract: In order to solve the problem of water resources allocation in inter-basin water transfer project, this paper puts forward an optimal water resources allocation model for rivers-lakes-pumping stations system by combining simulation technology and discrete differential dynamic programming(DDDP) on the basis of the conventional water resources allocation. The minimum water shortage and pumping water volume was taken as comprehensive objective function, and, the inflow and water use in different hydrological year were simulated and calculated based on certain operation rules of lake in order to determine the maximum available water supply volume and transferred water volume of each section. A dynamic programming model for joint operation of multiple lakes was proposed, in which the minimum pumping water volume of the whole system was set as the objective function, the water volume to be pumped into the lake or discarded water from the lake was expressed as decision variable and was solved by means of DDDP. The JiangSu section of South-to-North Water Transfer Project was taken as a study case, the results showed that not only the water supply guaranteed rate of the whole system can be improved but also the equilibrium allocation of water supply volume among each section and each period can be realized. The maximum transferred water volume 1408, 1418 and 1270 million m3 out of JiangSu province in 50%, 75% and 95% hydrological year were calculated, respectively. And the model decreased the total pumping water volume 5134, 9487 and 2819 million m3 in 50%, 75% and 95% hydrological year, respectively, which can reduce the cost of the water supply system through optimal operation, and finally realize optimal joint allocation of local and transferred water resources.