<p>Balancing agricultural decarbonisation with food security (FS) has become an important issue for major river-basin regions. Using the Yangtze River Economic Belt (YEB) as the research area, this paper analyses panel data for 11 provinces and municipalities from 2012 to 2024 to investigate the relationship between agricultural carbon emission efficiency (ACE) and FS. ACE is estimated using the super-efficiency SBM model, and FS is measured through a multidimensional indicator system based on the entropy method. The coupling–coordination model, relative development degree model, and Dagum Gini decomposition are then employed to evaluate coordination levels, relative development imbalance, and the sources of regional disparity. The results indicate that ACE rose markedly from 0.380 in 2012 to 0.940 in 2024, showing a transition from low-level fluctuation to steady improvement and then accelerated growth. FS also increased overall, from 0.568 to 0.628, although the improvement was accompanied by short-term fluctuations and clear provincial differences. The coordination between ACE and FS strengthened substantially over the study period. In 2012, several provinces were still characterised by imbalance or low-level transitional coordination, whereas by 2024 the YEB had generally moved towards a coordinated pattern. Nevertheless, differences in coordination level and relative development type remained across provinces. The Dagum Gini results further show that overall regional disparities narrowed, but inter-regional differences gradually became a more important source of spatial imbalance. These findings suggest that low-carbon agricultural policies in the YEB should be differentiated by regional conditions, while FS support and cross-regional governance should be strengthened to promote more balanced ACE–FS coordination.</p>