Abstract: China′s economy has shifted from rapid development to high quality development, and regional coordinated development is a significant strategic measure to promote high quality development of economy. Water Diversion Project from Yangtze River to Huaihe River is of strategic importance to water resource allocation and comprehensive utilization project. It would reconstruct and improve regional comprehensive transportation system and support regional coordinated development based on waterway transport between Yangtze River and Huaihe River. This paper studies the overall situation and navigation of the Water Diversion Project Yangtze River to Huaihe River, and summarizes comprehensive benefits in several aspects such as supporting water supply, developing navigation, improving ecology and the significance of developing navigation. Aiming at this problem of navigation development, this paper puts forward some suggestions for giving full play of the project’s navigation function, including making special planning of navigation, studying navigation in the river confluence, establishing and improving the navigation management system, comprehensive consideration of navigation development, paying attention to green development of navigation.