Physical water consumption (PW) in economic sectors are linked with virtual water consumption (VW) embodied in the supply chain of commodities. It is important to quantitatively assess PW and VW in economic sectors and understand interconnections between them for supporting water resources management. Here, we applied an IO framework to analyse how the PW is linked to the VW from both production and consumption perspectives. A water scarce region consisting of Ganzhou, Linze, and Gaotai counties (GLG) in the Heihe river basin in China is used as a case study. The agricultural sector is broken down into seven sub-sectors represented by individual major crops. From production perspective, the results show that the agricultural sector accounted for 98.1% of total PW, which can be divided into 79.0% of final demand driven water consumption and 21% of intermediate demand driven water consumption. From consumption perspective, the VW of all the sub-sectors in the agricultural sector was largely attributed to the direct VW. The sector “Food and tobacco processing” (the downstream of the agricultural sector) has the largest indirect VW among all the sectors. Most PW in GLG was used to produce the low value added primary agricultural products to fulfil the final demand (VW) outside GLG. The results suggest that the water resources management in arid regions should guide the restructuring of economy from increasing agricultural production to increasing the economic value of the embodied virtual water, and reducing the export of the virtual water from the low economic value products.