The modernization of ecological civilization and national governance capacity requires the acceleration of the reform of China's current water resourcs governance system. The China's water resource governance system is deeply analyzed, and it is believed that there are obvious problems such as immobilization of water distribution, weak awareness of ownership, administration of treatment measures and overlap of departmental functions in the China's water resource governance system which focuses on water allocation and water withdrawal permit. These problems are also the internal motives for the reform of the water resource governance system. It is put forward that the water right system is the manifestation of the property right system of modern natural resource assets in the field of water resource governance, and it is argued that the property right system of modern natural resource assetsis the institutional basis for the construction of the water resource governance system in the new era. Based on the three institutional modules of right, transaction, supervision of the property right theory, the reform orientation of the modern governance system of water resources is proposed. It is suggested that the modern governance system for water resources in the new era should be based on registration of right and regard the water right as the form of expression and the market mechanism as the core, and should properly handle the relationship among the water right system, water resource planning, ecological civilization construction, river(lake)chief system, horizontal ecological compensation of watersheds, financing of water conservancy projects and water withdrawal system. The deepening reform of the water resource governance system should be continuously promoted, and the establishment of a modern water resource governance system should be accelerated.