The multi-regional input-output model was used to quantify the water and energy footprints and their virtual flows, and an ecological network model based on virtual resource flows was constructed. The complex characteristics of the water-energy coupling system in nine provinces and autonomous regions of the Yellow River Basin were analyzed using indicators such as control allocation index and Finn cycle index. The results indicate that the regional resource footprint is closely related to the population and economic development level of the region. The energy footprint has good spatial consistency with energy production, while there is a mismatch between water footprint and water resource endowment. The virtual flow transfer network in the research area is extremely complex, with Henan, Shandong and other places being the main input areas for virtual flow, and Inner Mongolia and other places being the main output areas. The primary and secondary industries have a significant impact on virtual water and virtual energy flow, respectively. Affected by factors such as differences in industrial structure and development level, both water resources and energy systems show that the upstream and midstream regions are controlled by downstream regions, while competition dominates the ecological relationship between water resources and energy. The secondary industry in Sichuan and Inner Mongolia is a key regulatory target of the energy system, while the secondary industry in Shandong contributes significantly to the overall industrial drive of the region. The resource cycle efficiency and stability of the water resource energy coupling system in the provinces and regions are showing an increasing trend, with the stability of the water resource system being lower than that of the energy system. Therefore, it is necessary to optimize the water related industry structure appropriately to improve risk resistance capabilities.