The Yangtze River has unique ecological system and is China’s important economic warehouse. Presently and a long time in the future, the rebuilding of the ecological system of the Yangtze River should be put in the first place, there should be no big development but protecting the ecological system along the Yangtze River. How to realize ecological preference and green development? We have the following ideas such as implementing main body functional region strategy to optimize spatial development pattern, implementing urbanization strategy to use market-oriented manner to absorb the population in ecological fragile-area, perfecting spatial plan system to make spatial plan with “multi-regulation convergence”, moving industry into gardens and clusters to optimize industrial structure and spatial layout, and co-governance between the Upper Reaches and Lower Reaches of the Yangtze River to set up ecological compensation mechanism.