Water consumption, energy use, and carbon emission are three related key anthropogenic impacts on the natural environment. China is the largest carbon emitter and energy consumer, with the serious unevenly distributed water resources. Therefore, investigating the water–energy–carbon (WEC) nexus is important for China's environmental footprint reduction. This study explores the relation between water utilization, energy consumption, and carbon emission in China, based on a multiregional input–output (MRIO) analysis. The WEC nexus is discussed comprehensively in consideration of the utilization of water and energy and the emission of carbon, as well as the trade to and from and the consumption activities in different sectors and provinces. Results show that water, energy, and carbon present significant consistency in production and consumption processes. Sectors with higher consumption coefficients dominate the transfer of virtual WEC. Although virtual WEC mainly transfers from less developed regions to relatively developed regions, Category 1 (i.e., WEC all import) and category 2 (i.e., WEC disaccord) present opposite results to and category 3 (i.e., WEC all export) provinces in terms of W–E and W–C nexus. The net water and energy transfers are significantly positively correlated in category 1 provinces, whereas both sides are negatively correlated in category 2 and 3 provinces. This phenomenon also exists in the relationship between net water and carbon transfers. The virtual water, as well as energy and carbon export pressures are dispersed in these export provinces. Findings of this study are expected to assist the government in decreasing the environmental footprints and achieve sustainable development in China.