Agricultural intensification is a key pathway to enhance food security and resource-use efficiency, yet its integrated impacts on water, energy, and carbon emissions remain insufficiently understood. Under accelerating climate change and increasing water scarcity, elucidating the coupled relationships between agricultural intensification and water, energy, and carbon (WEC) footprints is critical for advancing sustainable agriculture. Here, we developed a spatial analytical framework integrating random forest-based crop yield prediction, evapotranspiration simulation, and bivariate local Moran's analysis to assess the interactions between agricultural intensification and WEC footprints for China's major grain crops at a 1 km x 1 km resolution. Both normal water-supply and water-stress scenarios were considered under representative concentration pathways. The results reveal pronounced spatial heterogeneity in agricultural intensification and WEC footprints, with higher intensification levels generally observed in southeastern China and lower in the arid northwest. The significant spatial clustering patterns were identified between intensification and WEC footprints, indicating strong coupling relationships. The coupling coordination analysis indicates that most provinces exhibit moderate to high coordination under normal water supply conditions, whereas water-stress scenarios lead to a substantial reduction in coordination levels, highlighting water constraints as a major limiting factor for sustainable intensification. This study elucidates the complex interactions between agricultural intensification and WEC nexus under current and future climate conditions. The findings highlight the necessity of improving production efficiency while reducing water stress, optimizing energy use, and mitigating carbon emissions, thereby supporting climate-resilient and low-carbon agricultural development.