Watershed is the most typical ecological area. It is also an important carrier for the construction of ecological civilization and the life community of mountains, rivers, forests, fields, lakes and grasses in China. The sustainable development of watershed plays a very important role in national economic and social development and ecological security. The increasingly tense relationship between man and land poses new challenges to the construction of ecological civilization and sustainable development of the river basin. This paper introduces the theories and methods of regional ecology and analyzes the key problems of regional ecology related to the sustainable development of river basins. The main ecological problems are summarized in the sustainable development of river basins in China. The countermeasures for sustainable development of river basins are put forward from four aspects, including the coordinated development of river basin ecological pattern-process-function, the realization of land-land coupling between river basins, the construction of human settlements and industrial structure suitable for ecological carrying capacity, and the establishment of ecological compensation mechanism. It is helpful to guide the rational development of river basins in China.