Population migration and aggregation of industrial factories in the process of urbanization in China has further increased water demand in the relatively developed areas of China. The existing water transfer projects couldn’t meet the increasing demand for water resources in water-scarce areas. The calculation of virtual water based on the input-output analysis and the implementation of reasonable virtual water transfer have become new approaches to relax the demanding pressure on regional water resources. This analysis used the regional inputoutput tables of the years 1997 and 2010 and the water resources bulletins of China to build a multi-regional inputoutput calculation model of virtual water and calculate the exchange relationships and transfer volumes among virtual waters of different industries in detail. This study also analyzed the association of regional virtual water flows with inter-regional population migration and geographic transfers of industries. The results showed that there were highly correlated relationships between the characteristics of regional population migration and virtual water spatial transfer in the context of urbanization in China. The geographic transfers of industries continue to affect the volume and direction of virtual water flows. In the future, researchers should consider the relationship between physical water transfers, virtual water flows, population migration and geographic transfers of industries in the context of urbanization to ensure the supply of water resources in China.