Virtual water trade (VWT) links local water withdrawal (WW) with distant consumption. Given the significant contradictions between China’s water demand and supply, it is urgent to clarify the responsibilities for WW (RWW) in VWT. Previous studies considering this responsibility have focused solely on the absolute volume of WW; however, the disparities in water availability and economic capacity lead to differing implications of the same WW action across regions. Here, to reassess the RWW, we introduce water scarcity index and value-added to WW and propose the concept of the three-dimensional water footprint (3DWF). We reveal the distribution distinction between WW and 3DWF among China’s regions. In addition, we explore how the 3DWF is transferred within the supply chain and further reveal its inequality and the contributions of regions to the inequality. We find that the distribution of 3DWF has changed dramatically compared to WW, primarily concentrating in China’s economic center. The 3DWF inequality primarily results from the distribution of 3DWF-local, with a Gini coefficient of 0.7556. Xinjiang has only 1.8% of the population but is responsible for 22% of the 3DWF-local in China and has become the largest contributor to the inequality. Notably, this inequality is mitigated when 3DWF-non-local is taken into account. Our findings provide new insights into the establishment of rigid constraints and the sustainable spatial deployment of water resources.