Based on the research paradigm of new structural economics, the theoretical relationship between urbanization and ecological environment is reconstructed. Theoretical analysis suggests that urbanization drives industrial structure upgrading and technological innovation and other production structure changes through natural resources, material capital, labor force, human capital and infrastructure and other endowment structure changes. With the different endowment structure and production structure of energy consumption and pollution properties, the main problems and characteristics of ecological environment in the process of urbanization are also different. From 1997 to 2018, the panel data at the provincial level in China were used to empirically test the theoretical viewpoints. Through a series of robustness tests and endogeneity treatment, the theoretical hypothesis of this paper is supported.