Abstract: The Yangtze River Economic Belt′s high-quality development is supported by the synergistic management of the three water issues, namely water resource-water environment-water ecology.Although the water quality of the mainstream riversin Yangtze River Basin has been improved, there are still a number of issues in tributaries and local areas, including difficult water resource regulation, frequent water environment pollution, and significant water ecological risks.It is critical to address the issue of synergistic governance and accurate regulation in an integral view on the water resources, water environment, and water ecology in the framework of building Yangtze River ecological civilization.This study analyses the problems regard to the three water issues in the Yangtze River Basin and the difficulties in cooperative regulation, and in view of the three water issues we propose some innovations and applications under the essential technical system of cooperative regulation including mechanism analysis, regulation and control strategy, and the development of smart basin.The results can promote the realization of a new pattern development of ‘high appearance' natural environment and ‘high quality' economic growth in the Yangtze River Basin, and to support the simultaneous improvement of water quantity, quality, and efficiency.