In the context of sustainable development, water resources, energy, and carbon emissions are pivotal factors influencing the rational planning of economic development and the secure establishment of ecological barriers. As a core food production area, how can the Great River Basin balance the pressure on the “water–energy–carbon” system (WEC) to realize the coordinated development of “nature–society–economy”? Taking the Yellow River Basin in China as the research object, this paper explores the coupling characteristics and virtual transfer trends of WEC in the agricultural sector under the condition of mutual constraints. The results show the following: (1) On the dynamic coupling characteristics, W-E and E-C are strongly coupled with each other. The optimization of water resource allocation and the development of energy-saving water use technology make the W-E consumption show a downward trend, and the large-scale promotion of agricultural mechanization makes the E-C consumption show an upward trend. (2) On the spatial distribution of transfer, there is an obvious path dependence of virtual WEC transfer, showing a trend of transfer from less developed regions to developed regions, and the coupling strength decreases from developed regions to less developed regions. The assumption of producer responsibility serves to exacerbate the problem of inter-regional development imbalances. (3) According to the cross-sectoral analysis, water resources are in the center of sectoral interaction, and controlling the upstream sector of the resource supply will indirectly affect the synergistic relationship of WEC, and controlling the downstream sector of resource consumption will indirectly affect the constraint relationship of WEC. This study provides theoretical and methodological references for the Great River Basin to cope with the resource and environmental pressure brought by global climate change and the effective allocation of inter-regional resources.
