<p>Water scarcity is an emerging threat to food security and socioeconomic prosperity, and it is crucial to assess the response of crop production to water scarcity in large river basins. The water footprint, which takes into account water use in supply chains, provides a powerful tool for assessing the contributions of water resources within a certain region, by tracking the volume and structure of virtual water flows. In this study of the structure of the water footprint network from a complexity perspective, we reassessed the significance of water resources for crop services in a large river basin with a severe water shortage -the Yellow River Basin (YRB) of China. The temporal increase of the complexity index indicated that the Virtual Water out-Flows (VWF) from the YRB were becoming increasingly critical to China; i.e., the ability of YRB to produce crops boosted difficulty of its water being replaced by water exporting from other basins. Decomposition of complexity suggested that during the 1980s to 2000s, the temporally increased complexity was due mainly to the paucity of competitors and the increasing uniqueness of crops supporting VWF. This complexity deeply embedded the YRB into the footprints of a water network that facilitated further development with constrained water resources, but it also reinforced reliance from other regions on YRB’s scarce water. Based on this analysis, we therefore suggest that resource regulation should be carried out at an appropriate time to ensure both the ecological sustainability and high-quality development of river basins.</p>