The report of the 20th National Congress of the Communist Party of China proposes to accelerate the green transformation of industrial development mode. Green transformation is based on the current status of industrial development and the carrying capacity of resources and environment, and it is crucial to explain and handle the relationship between industrial economic development and environmental system. Therefore, following the underlying logical chain of new structural economic theory and based on the perspective of new structural environmental economics, a theoretical analysis framework is constructed around the distortion of environmental structure caused by the deviation of industrial development mode from the principle of comparative advantage. The concept of green technology selection index is proposed to identify the comparative advantage of environmental factor endowment, analyze the endogenous and transmission mechanisms of industrial pollution and endogenous capacity, and propose relevant hypotheses. Empirical testing is conducted using provincial panel data of the chemical industry in the Yangtze River Economic Belt from 2007 to 2021. The research results indicate that deviation from the comparative advantage of factor endowment structure will lead to a lack of industrial viability and intensified pollution, leading to distortion of environmental structure. The distortion caused by the deviation of comparative advantage in environmental factors is more severe compared to production factors. The new structural environmental economics incorporates the environment into the input of production factors, redefines the regional factor endowment structure, and better adapts to the theoretical needs of current social and economic development. And the structural distortion in the development of the chemical industry in the Yangtze River Economic Belt exists under the pressure of environmental regulations and industry survival. In order to achieve sustainable development of the industry, the construction of a green transformation path for development needs to start from environmental factor endowment, and the government and enterprises should work together to generate the optimal structure through policy means and market mechanisms, forming a virtuous cycle.