Abstract: The construction of ecological waterways in the Yangtze River plays a pivotal role in fostering regional economic growth while harmonizing river ecology and navigation efficiency. It also serves as a valuable model for the global ecological transformation of river management. This paper systematically reviews the evolution of the ecological waterway concept and its practical implementation in the Yangtze River Basin. From a river functionality perspective, it redefines the “waterway” as a functional zone delineated based on navigation needs, rather than as a physical river entity. Building on insights from Yangtze River waterway regulation projects, the study identifies two primary challenges in current ecological waterway development: the lack of systematic planning for ecological measures and the complexity of evaluation frameworks. To address these issues, the paper proposes optimization strategies in three key areas: enhancing the scientific precision of functional zoning, integrating ecological principles into technical systems, and streamlining evaluation frameworks to focus on core ecological functions of rivers. By promoting a dynamic balance between navigation and ecological functions, refining zoning and technical coordination, and establishing concise and targeted assessment frameworks, the study highlights pathways to achieve a sustainable alignment of navigation efficiency and ecological preservation. This research provides a robust theoretical foundation for the sustainable development of ecological waterways in the Yangtze River and offers actionable insights for advancing ecological river management worldwide.