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Improving total factor carbon emission efficiency (TCE) is the key to achieving carbon emission reduction targets while ensuring economic growth. In this paper, the global Malmquist index based on the SBM model is used to measure TCE of 283 cities in China from 2011 to 2019. On this basis, this paper uses the spatial econometric model and intermediary effect model to empirically analyze the impact of industrial co-agglomeration on TCE and its transmission mechanism. Furthermore, considering the differences in geographical location and resource endowment among regions, this paper analyzes the heterogeneous effect of industrial collaboration agglomeration on TCE in different regions and cities. The results show that: (1) Industrial co-agglomeration can improve TCE, and its main transmission channel is technological innovation. (2) Industrial co-agglomeration has a positive spatial spillover effect. Industrial co-agglomeration in one region can improve the TCE in the surrounding regions. (3) Industrial co-agglomeration of cities with different geographic locations and resource endowments has a heterogeneous effect on TCE. Regarding geographical heterogeneity, the industrial co-agglomeration in the eastern region has the greatest promoting effect on TCE, followed by the central region. However, the impact of industrial co-agglomeration in the western region on TCE is not significant. Regarding resource endowment heterogeneity, the industrial co-agglomeration in non-resource-based cities has a greater promoting effect on TCE than that in resource-based cities. [ABSTRACT FROM AUTHOR]