How to optimize the stress structure of water resources is a binding issue for the Yangtze River Economic Belt to continue to support the high-quality development of the national economy and society of China during the 14th Five-Year Plan period. In the background of “joint protection and cautious exploitation”, the stress index method and the multi-regional input-output model are used to analyze the structural characteristics of water resource stress and the contribution of virtual water flow to the regional stress in the Yangtze River Economic Belt from 2002 to 2019 from the perspective of virtual water. The results show that there are significant gaps in the actual annual average stress and the changing trend among the provinces and cities in the Yangtze River Economic Belt. The stress values in Shanghai and Jiangsu are much higher than those in other provinces and cities, and they are strongly dependent on the transiting water. The virtual water in Jiangsu, Anhui, Hunan, Hubei and Jiangxi mainly presents the state of net internal outflow, and the net outflow of virtual water in Anhui and Jiangxi exhibits an upward trend. In general, the virtual water transfer implied by trade has made a greater contribution to alleviating the water resource stress in Shanghai, Zhejiang and Chongqing. However, it exerts increasing pressure on Anhui, Jiangxi, Hubei and Hunan. Finally, some suggestions are put forward for the regional spatial balance of water resource stress in the Yangtze River Economic Belt, including establishing a scientific industrial structure and further promoting water conservation, improving the internal and external trade structure of the region, and coordinating the outflow of virtual water and physical water.