The shortage of water and energy are hindering the rapid development of the regional economy in recent years. Therefore, exploring the synergy of water and energy and managing the two resources comprehensively is conducive to the sustainable development of the economy. Based on the multi-regional input-output (MRIO) model, this study proposed a new assessment framework for investigating the water-energy (WE) relationship. We used this novel framework to identify the relationships in different sectors. The achieved results are as follows. First, water and energy are closely related in many sectors, including agriculture, extractive sector, petroleum, coking, and nuclear fuel processing sector, and other sectors. However, the construction sector, textile and clothing sector, and wood processing and furniture manufacturing sector showed low correlation (p > 0.05). Second, on the whole, the WE relationship has been improving. Among the eight regions, the relationship varies greatly, and the Southern coastal region has the best relationship (r = 0.78). Third, the spatial distribution of water and energy footprints shows high agreement. Although the virtual water and energy flows alleviated the energy pressure in Coastal areas, it has aggravated the water and energy shortages in Central areas. Therefore, identification of key sectors and construction of suitable policies may help alleviate the contradiction between water and energy shortages and drive regional economic development.