Virtual water flows have a profound impact on the natural water system of a country or region, and they may help conserve local water resources or exacerbate water scarcity in some areas. However, current research has only focused on the measurement of virtual water flows, without analysis of the causes of virtual water flow patterns. This study first obtained virtual water flow patterns across provinces by constructing a multi-regional input–-output (MRIO) model of the Yellow River basin in 2012 and 2017, and then analyzed its driving factors by applying the extended STIRPAT model to provide directions for using virtual water trade to alleviate water shortages in water-scarce areas of the basin. We found the following: (1) The Yellow River basin as a whole had a net virtual water inflow in 2012 and 2017, and the net inflow has increased from 2.14 billion m3 to 33.67 billion m3. (2) Different provinces or regions assume different roles in the virtual water trade within the basin. (3) There is an obvious regional heterogeneity in the virtual water flows in different subsectors. (4) Per capita GDP, tertiary industry contribution rate, consumer price index, and water scarcity are the main positive drivers of virtual water inflow in the Yellow River Basin provinces, while primary industry contribution rate, per capita water resources, and water use per unit arable area promote virtual water outflow. The results of this paper present useful information for understanding the driving factors of virtual water flow, which could promote the optimal allocation of water resources in the Yellow River basin and achieve ecological protection and high-quality development in this area.