Drawing upon the data of China’s animal husbandry industry from 2000 to 2020 in 30 provinces, an EBM model incorporating non-desired outputs was employed to gauge the carbon emission efficiency of the animal husbandry industry. Coupling degree models, spatial autocorrelation models, and Markov chain models were utilized to assess the coupling degree between the industrial agglomeration of the animal husbandry sector and its carbon emission efficiency, and to analyze its spatio-temporal distribution and evolution. The outcomes showed that (1) the coupling degree of China’s animal husbandry industry agglomeration and carbon emission efficiency exhibited an overall downward inclination. Notably, the diminishing tendency of the coupling degree was more pronounced in the eastern, central, and western parts of the country; (2) the coupling degree of the 30 provinces showed a spatial distribution of “western > central > northeast > eastern”; (3) the coupling degree showed obvious agglomeration distribution characteristics, wherein a substantial quantity of provinces was located in high–high clustering zones and low–low clustering zones; (4) the coupling degree of various provinces remained fairly stable, but after considering the spatial and geographical correlation, the coupling degree of each province would be influenced by the coupling degree of its adjacent provinces. Evidently, there remained a substantial scope for the enhancement of the coupling coordination degree between the industrial agglomeration of China’s animal husbandry and the carbon emission efficiency. This research is capable of furnishing a theoretical allusion for promoting regional cooperation, leveraging agglomeration advantages, and implementing carbon emission abatement regimes and directives to enhance the low-carbon development level of animal husbandry industry agglomeration in China.
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