As the embodiment of human activities, the change of regional industrial structure is an essential driving factor of global environmental change. Consequently, the research on the change of regional industrial structure and associated effects on the environment is one of the key issues of researches on sustainable development, human-environment relationship, and regional response to global environment change. However, compared to the flourish of researches on environmental impact assessment of industrial departments, few studies have been conducted to assess the environmental impact of regional industrial structure. In this study, based on a synthetic analysis of environmental disturbances of different industrial departments, the environmental impact coefficient of industrial department associated with the index of environmental impact of industrial structure was constructed, so as to make a quantitative assessment of environmental impact of the change of regional industrial structure. And the results of the case study in Lijiang City, a rural region of China, have showed that there are two obvious changes of industrial structure in the study area from 1992 to 2003, associated with a continuous decreasing of the index of environmental impact of industrial structure, which indicated a positive environmental effects of the change of regional industrial structure.