Virtual water exerts an indispensable influence on water resources, yet the existing studies on the water rights allocation of transboundary rivers hardly consider virtual water transfer (VWT). Therefore, in this paper, we used Taihu Lake as an example with data collected in 2017 that described both physical and virtual water use. We used these data to evaluate water rights allocation schemes by coupling virtual and physical water use. In order to achieve this goal, we first determined the physical water rights allocated for the four regions connected to the Basin. Next, we employed the multi-regional input–output (MRIO) approach to calculate the VWT among the four regions; then, we converted the VWT to the riparian level via the water efficiency coefficient. Finally, with virtual water included in the physical water rights allocation, we formulated a final water rights allocation for Taihu Lake. The results showed the following findings: (1) The ranking of the amount of physical water rights allocation is: Jiangsu > Zhejiang > Shanghai > Anhui. (2) Anhui and Jiangsu produce a net export of virtual water (2.259 billion m3 and 1.78 billion m3, respectively), while Zhejiang and Shanghai have a net import of virtual water (2.344 billion m3 and 1.695 billion m3, respectively), indicating that Anhui houses more water-consuming industries and is in greater need of economic restructuring. (3) The integration of virtual water makes a difference: Jiangsu achieved 16.208 billion m3 in terms of the amount of water rights allocated, Zhejiang achieved 6.606 billion m3, Shanghai achieved 3.040 billion m3, and Anhui achieved 4.319 billion m3, with a ranking of Jiangsu > Zhejiang > Anhui > Shanghai. The results detailed above prove that virtual water exerts an indispensable influence, and integrating virtual water can make the physical water rights allocation of transboundary rivers more equal and reasonable.