In this paper, we aim to explore the coupling coordination and influence factors of recessive farmland use transition (RFUT) and agricultural carbon emissions (ACEs) in the Yangtze River Economic Belt (YREB), so as to provide decision-making reference for cultivated land protection and high-quality agricultural development. This paper used comprehensive evaluation method to measure the RFUT level in the YREB, evaluated the coupling coordination degree between the RFUT and ACEs, and further established a spatial econometric model to explore its influence factors. The results show that: (1) The RFUT level in the study area showed a steady development trend from 2001 to 2021, and the high-value areas gradually expanded from the downstream to the middle and upper reaches over time. (2) The ACEs in the study area first increased and then decreased, with small fluctuations. Moreover, the high-level areas were mainly distributed in the middle and lower reaches, while that was low and stable in the upper reaches. (3) The coupling coordination degree between the RFUT and ACEs in the YREB was constantly improved, showing a spatial pattern of higher in the east and lower in the west. (4) The value of coupling coordination degree showed a phenomenon of high-high and low-low agglomeration, which had a significant positive spatial effect. Natural, economic and social factors affect the level of coupling coordination degree, and the spillover effect of each factor on the neighborhood unit was more obvious. We should pay attention to the spatial demonstration effect of the RFUT and ACEs in the YREB, and build low-carbon and efficient policies for cultivated land use and agricultural development according to the local conditions.