In China, the water resources problems in key economic regions, such as the overexploitation of groundwater and the occupation of the ecological water and the agricultural water from the urban and industrial development, are induced by the uneven spatial-temporal distribution of water resources. By the optimized allocation of the water resources, the inter-basin water transfer projects have improved the living conditions and ecological environment of the water shortage region, and ensured the sustainable development of economy and society. In this paper, with the practical case of the water diversion for central area of Yunnan, the optimum process of planning scheme on water transfer project are discussed from the aspects of the necessity of water transfer, the range of intake area, the project scale and the project layout.