We conducted a quantitative analysis of the relationship between the evolution of China's industrial structure and environmental change. Using the industrial structure characteristic bias index and data from 29 manufacturing industries in each province from 1995 to 2010, we described the impact of pollution-emission characteristics of industry structure on the regional environment. The results show that wastewater-discharged characteristic of industrial structure in the northwest and central areas declined from 1995–2010, but this trend has weakened. The industrial structure of southwest and southeast areas had a high level of solid waste discharge and a constantly strengthening trend in SO₂ emissions. We also analyzed the growth and recession of each sector in eight regions in China from 1995 to 2010. Among the eight regions, the middle reach of the Yellow River, and northwest and southwest China had a clear increasing trend of high pollution industries; the eastern coast, southern coast, middle reach of the Yangtze River and northeastern China did not sustain an increase in high pollution industries. In addition, regression analysis modeling was used to analyze the impact of the evolution of industrial structure on the disparities of regional environmental effects. We found that regional industry structure was closely related to environmental quality, especially for western areas at lower stages of economic development. In the future, all regions must prevent and forefend the risk of environmental pollution in the update and adjustment of industrial structure.