Abstract: Intensive industrial enterprises, unreasonable industrial structure and layout have caused cumulative and potential ecological problems and environmental risks, which have become the bottleneck of sustainable and green development in the Yangtze River Economic Belt. Based on the characteristics of natural resources, the current economic and social development situation, and the industrial development phase of the Yangtze River Basins, this paper selects three typical river basins to conduct in-depth research. The environmental risks of the three typical river basins are: (1) There are layout contradictions between the heavy chemical industry below Hukou basin of the Yangtze River with the most intensive heavy chemical industry and the densest population. (2) There are government program contradictions between key industrial development and national and provincial water transfer project in the middle and lower reaches of the Hanjiang River. (3) There are contradictions between development and protection in the Wujiang River Basin that has high development intensity of phosphate rock resources and is located in a karst landform area with fragile ecosystem. Different environmental risks and the trend of heavy chemical industry layout and regional comprehensive development strategy in the typical basin are analyzed. Based on goal-oriented (goal of the Yangtze River environmental protection) and problem-oriented process (solving the problems between the living spaces and industrial spaces in the Yangtze River Economic Belt), complied with the general idea of 'keeping the bottom line, optimizing the layouts, improving quality and ensuring safety', this paper aims to ensure that the goals of 'Clean Yangtze River' and 'Safe Yangtze River' are achieved. As a reference for the accurate protection strategies and management measures of the Yangtze River Economic Belt, this paper proposes optimal measures for the green development of heavy industries and recommendations for differentiated ecological environmental protection of the typical watersheds of the Yangtze River Economic Belt: (1) The main stream below the Hukou of the Yangtze River should ensure the safety of human-being, optimizes the layout with industrial parks, improve the capacity of regional environmental risk prevention, and study the countermeasures for persistent organic pollutants control in the Yangtze River coastal area; (2) The Hanjiang River Basin should take the environmental capacity of the basin as the hardcore constraint, adjust the national industrial policy strategy in the middle and lower reaches of the Hanjiang River, and strictly control the high-water consumption and high-water pollutions industries; (3) The Wujiang River Basin should ensure the water quality of the downstream reservoir area, strictly control the new phosphorus chemical plants in the karst landform area, and study the implementation of the special discharge limit of phosphorus in the karst area.