Abstract: This study estimated the carbon emission, carbon sink and net carbon emission effect of the agri-food system from an industrial perspective in Yunnan Province from 2013 to 2022 using emission factor method. Then investigated the influencing factors of carbon emission in the agri-food system using Logarithmic Mean Divisia Index (LMDI) model for decomposition analyses. The results indicated: (1) The carbon emission and net carbon emission effect fluctuated and decreased while the carbon sink increased steadily, in which the carbon emission from animal husbandry (61.87%) had the largest proportion and is the main industry affecting the carbon emission of the agri-food system. The carbon emission of plantation industry and food industry account for 22.42% and 14.82%, respectively. (2) The decomposition analyses of influencing factors showed that, the contribution of production efficiency, industrial structure, energy consumption intensity, and labour population size to the carbon emission of agri-food system was negative, in which the contribution of energy consumption intensity to inhibit the carbon emission was 47.32%. In contrast, energy economic efficiency, financial input, and economic level were shown to be able to promote the carbon emission of the agri-food system. Yunnan Province should reduce carbon emissions from animal husbandry, encourage the diversification of crop cultivation and develop low-carbon food processing, reduce the use of traditional coal, improve energy efficiency, strengthen the correlation between financial investment and energy consumption intensity, further develop clean energy technology, and achieve carbon reduction and efficiency increase in agricultural food system.