Water management is one of the key problems to the soci-economic development and eco-environment construction of endorheic drainage in the northwestern of China. Therefore, one of the important mission we are facing is how to make effective water management, particular in the northwestern inland river. By analysing the conditions of Heihe river basin in China and the Murray-Darling river basin in Australia, we explored the water management of these two rivers through comparative analysis, and theoretically provided the methods and plans for the water management system of Heihe river basin. Meanwhile, a set of measures were suggested:optimizing the structure of water use to improve economic returns, attaching great importance to the unified management to realize the optimal allocation of water resources, strengthening the organizational management to formulate the river basin law, and encouraging the public to participate in the water management of the river basin, further deepening the reform of water right system.