Energy security, food security, and water security have become the three most prominent problems in human survival and sustainable development. The three are interrelated and directly affect each other; that is, there exists a nexus between, energy, food, and water (EFW). A scientific understanding and correct response to this is important for achieving the sustainable development of natural resources. This study uses quantitative analysis to estimate the Central China region's energy-food production water footprint (WF) and virtual trade water flow from 2001 to 2016. It proposes a Modified Water Stress Index (MWSI) associated with virtual water outflows and evaluates the pressure exerted by virtual water flowing out, along with the effect of trade on local water resources systems. The results indicate that the energy and food production WF and virtual trade water flow are on the rise, causing water stress in local and export areas. Based on the adjustment of industrial structure, optimization of production technology, and rational regionalization of ecological divisions, the paper makes comprehensive policy recommendations to ensure the region's sustainable development of water resources for the future.