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Given the great number of studies focusing on the temporal interaction between economic and environmental subsystems, it is useful to perform a quantitative spatial assessment of these subsystems. In this paper, comprehensive assessment indicators for regional economic development and environmental pollution subsystems are constructed. Then, the degree of coupling and coordination of the regional economy-environment system is calculated for 350 prefectural units in China. It is found that the economic development and environmental pollution in most prefectural units is still at a low level of coupling and coordination. According to the coupling and coordination values, the Chinese territory can be divided into four types of area: economy-environment harmonious area, economy-environment gearing area, economy-environment rivaling area and low coupling degree of economy-environment area. Based on a structural analysis of the industrial sector in the four types of areas, there is a spatial relationship between the regional industrial sector structure and the coupling-coordination level. In the economy-environment harmonious area, the sectors of manufacturing of high-technology and high value-added products, such as communications, computer and electronic equipment, transport equipment and electrical machinery, account for a large proportion of the value of local industrial output. The industrial value of the economy-environment gearing area is concentrated on the manufacturing of machinery and equipment, and contains a few polluting sectors such as ferrous and non-ferrous metallurgy, chemical manufacturing and electricity generation. The economy-environment rivaling area is the type of area where polluting sectors concentrate, such as iron and steel, petrifaction, coal mining, building materials and electricity generation. In the low coupling degree of economy-environment area, its industry is concentrated on the production and processing of primary products.