Water utilization, energy consumption, and carbon emissions are mutually intertwined and play vital roles in agricultural supply chains. Identifying the water-energy‑carbon (WEC) nexus relationships along with its driving forces is of great importance to alleviate resource scarcity and advance a green economy. This study utilizes multiregional input–output (MRIO) analysis and proposes a new indicator, nexus intensity, to investigate the relationship among water, energy, and carbon flows in agricultural trade; furthermore, it modifies the gravity trade model to explore the hidden driving forces for the WEC nexus. The Regional Comprehensive Economic Partnership (RCEP) countries are used as a case study, and the results show that large volumes of WEC flow roughly from the southeast to the northwest. China plays an active role in agricultural trade, contributing 53.34%, 62.00%, and 64.09% of RCEP agriculture-related water utilization, energy consumption, and carbon emissions, respectively. For nexus intensity on the production side, countries with less agriculture-related WEC tend to have extreme situations of extreme resource utilization or emissions. Such situations have become more balanced on the consumption side. Exporters exert a greater impact on agricultural trade than importers. Small population countries such as Australia, New Zealand, and Cambodia serve as granaries for other countries. In addition, countries with higher carbon emissions tend to import carbon-intensive products from other countries. By analyzing the linkages between water, energy, and carbon associated with agricultural products and excavating driving forces, this study provides insights for nexus management on improving resource use efficiency and reducing carbon emissions through transnational trade.