Water conservation and carbon reduction are key challenges for the sustainable development of agriculture in the Yangtze River Economic Belt, and coupled with research on the water-carbon relationship of farmland ecosystems can help to clarify the sustainability of agricultural water resources and elucidate the pattern of agricultural carbon emissions, and provide decision-making support for the management of water resources for agricultural production and low-carbon sustainable development. This paper evaluates the carbon footprint of farmland ecosystems in the Yangtze River Economic Zone from 2011 to 2020 from the perspective of carbon and water correlation, based on the theory of carbon and water footprints, introduces the breadth and depth of footprints, and utilizes the coupling coordination degree model to explore the coupling relationship between carbon and water footprints of farmland ecosystems. The results show that: (1) the farmland ecosystems in the Yangtze River Economic Zone are in the stage of carbon deficit and water surplus, with the highest carbon deficit in Sichuan Province and the highest water surplus index in Hunan Province. (2) The carbon footprint of farmland ecosystems in the Yangtze River Economic Zone exhibits an overall trend of initial increase followed by a decline., with the highest level in Sichuan Province and the lowest in Shanghai, and the high value area is mainly concentrated in the upper reaches of the Yangtze River Economic Zone; except for Guizhou Province, the carbon footprint depth for all other provinces equals 1, and there is no need to utilize the stock of capital. The breadth of the water footprint shows a fluctuating downward trend, with the highest in Jiangsu and the lowest in Shanghai; except for Jiangsu, the depth of the water footprint of the remaining 10 provinces is equal to 1, without the need to utilize the capital stock of water resources.(3) From the value of the coupling degree of coordination, the coordination between the carbon and water footprints of farmland ecosystems in the Yangtze River Economic Zone has shown a trend of annual increase, but the overall coupling degree of coordination is not high enough in the time dimension; from the spatial dimension, the average value of the coupling degree of the carbon and water footprints is distributed in the form of "upstream>middle reaches>downstream". (4) There is a spatial dependence on the coupled and coordinated development level of the carbon and water footprint in the Yangtze River Economic Zone, and the spatial correlation is unstable and fluctuates greatly, which is mainly manifested in the increase in the number of high-high agglomerations, fewer high-low agglomerations, and more stable low-low and low-high agglomerations.