Undergone five years of eco-environmental governance and green transformation in social-economic development, remarkable achievements have been made in the exploitation and protection of water resources of the Yangtze River. Nevertheless, the negative impact of extensive economic growth in the past four decades could not be eradicated in a short term. The ecological environment in the Yangtze River is still facing daunting tasks in complicated circumstances, which have restricted the sustainable development of the Yangtze River Economic Belt. To promote green development and realize a win-win situation between economic development and eco-environmental improvement are new requirements and challenges for the green development of the Yangtze River Economic Belt. In this paper, we identified the deficiencies in exploiting and protecting water resources in the Yangtze River from the perspective of green development. With ecology as priority and green development as guiding principle, we put forward the major tasks and priorities of a systematic protection accommodating green development. The objectives of protection work are being efficient, moderate, balanced, and harmonious. The paper is expected to offer reference for exploring the new path of green development in the Yangtze River Economic Zone with ecology as priority.