Research on the Yellow River Basin’s virtual water is not only beneficial for rational water resource regulation and allocation, but it is also a crucial means of relieving the pressures of a shortage of water resources. The water stress index and pull coefficient have been introduced to calculate the implied virtual water from intraregional and interregional trade in the Yellow River Basin on the basis of a multi-regional input–output model; a systematic study of virtual water flow has been conducted. The analysis illustrated that: (1) Agriculture is the leading sector in terms of virtual water input and output among all provinces in the Yellow River Basin, which explains the high usage. Therefore, it is important to note that the agricultural sector needs to improve its water efficiency. In addition to agriculture, virtual water is mainly exported through supply companies in the upper reaches; the middle reaches mainly output services and the transportation industry, and the lower reaches mainly output to the manufacturing industry. Significant differences exist in the pull coefficients of the same sectors in different provinces (regions). The average pull coefficients of the manufacturing, mining, and construction industries are large, so it is necessary to formulate stricter water use policies. (2) The whole basin is in a state of virtual net water input, that is, throughout the region. The Henan, Shandong, Shanxi, Shaanxi, and Qinghai Provinces, which are relatively short of water, import virtual water to relieve local water pressures. However, in the Gansu Province and the Ningxia Autonomous Region, where water resources are not abundant, continuous virtual water output will exacerbate the local resource shortage. (3) The Yellow River Basin’s virtual water resources have obvious geographical distribution characteristics. The cross-provincial trade volume in the downstream area is high; the virtual water trade volume in the upstream area is low, as it is in the midstream and downstream areas; the trade relationship is insufficient. The Henan and Shandong Provinces are located in the dominant flow direction of Yellow River Basin’s virtual water, while Gansu and Inner Mongolia are at the major water sources. Trade exchanges between the midstream and downstream and the upstream should be strengthened. Therefore, the utilization of water resources should be planned nationwide to reduce water pressures, and policymakers should improve the performance of agricultural water use within the Yellow River Basin and change the main trade industries according to the resource advantages and water resources situation of each of them.