ABSTRACT Urban economic development benefits from industrial agglomeration by enhancing efficiency, but it may also bring negative effects, such as environmental pollution. This research uses data from 283 Chinese cities from 2007 to 2019, and applies the Spatial Durbin Model to investigate the spatial effects of industrial agglomeration on carbon emission efficiency, along with its impact mechanisms at various stages of collaborative agglomeration between the manufacturing and service sectors. The results indicate that: (1) The upgrading of the service industry from consumption-oriented to production-oriented has proved to be conducive to enhancing carbon emission efficiency and alleviating the environmental problems associated with manufacturing agglomeration. (2) The industrial collaborative agglomeration exerts a spatial spillover effect on carbon emission efficiency. Over time, as the degree of industrial collaborative agglomeration reaches a specific threshold, it positively impacts the carbon emission efficiency within the local area but exerts an inhibitory effect in neighboring regions. (3) The urban agglomerations of Yangtze River Delta, Beijing-Tianjin-Hebei, and Pearl River Delta regions, along with low-carbon pilot cities, demonstrate a greater capacity to enhance the positive impact of industrial collaborative agglomeration on carbon emission efficiency. (4) Collaborative industrial clustering fosters technological progress through domestic technology transfer and green technology innovation. It also mitigates mismatches between labor and capital, enhances land-intensive utilization efficiency, and optimizes resource allocation, ultimately leading to improve carbon emission efficiency. This research contributes to China’s economic and social transition towards a low-carbon future and provides valuable insights for the green development and industrial upgrading of developing countries.