Abstract: Farmers’ professional cooperatives can integrate the resources of scattered small farmers, innovate business models, and provide a feasible path for the green and low-carbon transformation of agriculture. Based on panel data from 30 provinces in China from 2007 to 2022, this paper constructs a comprehensive evaluation system of agricultural carbon emission efficiency covering the full chain of “input–emission–sequestration”. The super-efficiency SBM model is used to measure agricultural carbon emission efficiency, and the two-way fixed effect model and mediation effect model are employed to systematically analyze the impact and mechanism of the development level of farmers’ professional cooperatives, with agricultural management scale and agricultural mechanization serving as mediating variables. The results show that: 1) the development of farmers’ professional cooperatives significantly improves agricultural carbon emission efficiency, and this conclusion remains robust after endogeneity treatment and robustness tests; 2) the effect mainly operates through two mediating paths, namely expanding agricultural management scale and enhancing agricultural mechanization; 3) heterogeneity analysis indicates that the promoting effect is more significant in main grain-producing and grain-selling areas as well as in regions with low topographic relief, and is particularly strong for planting and service-oriented cooperatives, as well as cooperatives led by farmers and those engaged in integrated production and marketing. Based on these findings, farmers’ professional cooperatives should be fully leveraged to improve agricultural carbon emission efficiency and accelerate the green and low-carbon transformation of agriculture.