Under the dual pressure of industrial structure upgrade and atmospheric environment improvement, China, in a transition period, is facing the challenge of coordinating the relationship between the industry and the environment system to promote the construction of a beautiful China. Based on system theory and coupling coordination model, the interaction analysis framework between industrial structure (IS) and atmospheric environment (AE) was constructed. An integrated system with 24 indicators was established by the pressure–state–response (PSR) model of IS and level–quality–innovation (LQI) model of AE. Then, we analyzed trends observed in coupling coordination degree (CCD) and dynamic coupling coordination degree (DCCD) for 11 cities in Zhejiang Province, China, using statistical panel data collected from 2006 to 2017. Conclusions were as follows: (1) the 11 cities’ comprehensive level of the IS system shows a trend of stable increase, yet the comprehensive level of AE demonstrated a trend of fluctuation and transition. There are significant spatial variations among cities; (2) The CCD analysis results found that Hangzhou, Ningbo, and Wenzhou take the lead in realizing the transformation from barely coordinated development to superior coordinated pattern, while other cities were still in the stage of barely coordinated development; (3) the DCCD phase of 11 cities can be roughly divided into three types: upgraded—utmost development type (only Hangzhou), stable—harmonious development type (Wenzhou, Lishui, and Zhoushan) and transitional—harmonious development type (the remaining seven cities). This means, for most cities, the contradiction between the transformation process of IS and the AE has become increasingly prominent and intensified. Finally, three necessary and sustainable strategies were proposed to environmental policy makers.
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