The production of traditional agricultural products of the Yangtze River Economic Belt, such as rice and potatoes, accounts for more than 50% of the national total in China. The agricultural carbon emissions directly affect the green development of the region. From a system’s point of view, the interactions of water, land, energy, and carbon was comprehensively considered, and based on this, spatial and temporal differences of agricultural carbon emissions in the Yangtze River Economic Belt and its impact factors were studied. (1) At the meso-level, agricultural carbon emissions of the Yangtze River Economic Belt from 2009 to 2016 were calculated, and the matching degree of water and land was calculated to lay the foundation for the introduction of water and land elements into Kaya’s identity. (2) With the help of logarithmic mean divisia index method, contribution values of impact factors of agricultural carbon emissions were discussed. The results show that: (1) From 2009 to 2016, the overall agricultural carbon emissions of the Yangtze River Economic Belt showed a staged upward trend, with a growth rate of 16.43% from 1208.7398×10 4 t in 2009 to 1407.2846×10 4 t in 2016, and the proportion of agricultural carbon emissions in Hunan, Jiangsu, Zhejiang, and Hubei provinces reached 59.32% in 2016; (2) For the Yangtze River Economic Belt as a whole, agricultural carbon emissions intensity, agricultural land and water use ratio, and per capita arable land area are inhibitory factors for agricultural carbon emissions, while economic output of agricultural water resources and population factors are contributing factors; (3) At the provincial level of the Yangtze River Economic Belt, the effects of impact factors on agricultural carbon emissions are different, especially the agricultural land and water use ratio, which plays a promoting role in Hunan, Sichuan, Guizhou, and Yunnan provinces, but a inhibiting role in Shanghai and Jiangsu, Zhejiang, Anhui, Jiangxi, and Hubei provinces and Municipality. Provinces with high matching degree of water and land (MDWL) have relatively higher inhibiting effect on agricultural carbon emissions compared with provinces with low MDWL. Based on this, it is proposed that water, land, and energy elements should be comprehensively considered to formulate low-carbon agriculture development strategies and combine low-carbon development of agriculture with water-saving, energy-saving, and conservation and utilization of cultivated land.