Having terrain feature of two basins between three mountains, Xinjiang is divided into North Xinjiang, South Xinjiang and East Xinjiang. Tarim River Basin almost covers the whole of area of South Xinjiang, made by nine water systems such as Hetian River, Yarkant River, Akesu River and so on. The paper analyzes its current situation of geography, climate, environment, oasis economic characteristics, water resources and exploration& development. It researches current water problems,including further increasing the contradiction of water supply and demand, a new threat causing by pollution of surface water and ground water to water ecological environment protection, climate change and transboundary rivers water affairs conflict, etc. It predicts challenge that will face in the future, including more complex of water resources problems, entering a new phase of construction and management of water facilities, river basins' water function recovery becoming a long term work, implementing trans-basin water transfer, etc. It proposes tentative plan of construction works of New Qiuci Project and New Loulan Project, Ecological-type construction in Tarim River, Hetian River discharge water quantity replacement scheme, and arid inland rivers threshold value regulation & control management model, which means half water for environment and half water for economic development while 30% runoff is used for natural water cycle and the maximum utilization ratio of inland surface water is not more than 70% in which there is 30% for water consumption for artificial environment and 70% for social and economic development. It provides a new way for Tarim River Basin comprehensive treatment and South Xinjiang stable development in the aspect of inter-basin water transfer, enhancing carrying capacity of water resources and environment, optimizing social and economic development layout, constituting ecological and economic zone of Tarim Basin, ecological immigration, relieving resources pressure for environment caused by population in the oasis, pushing balance development of national reunification and so on.