Water, energy, and food are fundamental resources for human survival and socioeconomic development, forming a tightly coupled Water-Energy-Food (WEF) nexus system. In arid and semi-arid regions, this nexus faces particularly severe challenges due to harsh environmental conditions and limited resources endowments. To uncover the internal interactions and sustainability status of the WEF system, this study took Ningxia, China as a case to quantify resource flows and construct a spatial ecological network model applicable to arid and semi-arid regions. Through systematic analysis of ecological network control, utility, hierarchy, and robustness, we identified the interaction mechanisms and evaluated system sustainability. The results indicated that: 1) There was significant spatial differentiation in the dominant controlling subsystems: irrigation areas were dominated by water and energy subsystems (control intensity 63%-66%), whereas sandy and mountainous areas were controlled by the food subsystem. 2) Ecological relationships were predominantly exploitative (35%) and predation (30%), with mutualism accounting for only 15%, and showed clear spatial heterogeneity: water-energy mutualism occurred in mountainous areas, while predation and exploitation characterized the water-energy relationship in irrigation and sandy areas. 3) The food subsystem exhibited both the strongest pulling force (42.29%) and driving force (24.29%), yet its regional role presented a dual dilemma: a "high pull-high ecological cost" pattern in irrigation areas versus a "strong drive-low economic scale" pattern in mountainous areas. 4) Robustness analysis revealed a widespread "high productivity-high vulnerability" paradox (optimal robustness /3 = 0.3701). Irrigation areas showed the highest robustness (/3 = 0.6369), some mountainous areas approached the optimum, while Hongsibao (sandy areas, /3 = 0.23) and Jingyuan (mountainous areas, /3 = 0.17) were the most vulnerable. By applying ecological network analysis, this study translates the abstract nexus concept into a spatially explicit diagnostic framework. The revealed structural imbalances and robustness paradox provide an important theoretical basis and decision-support for differentiated precision governance of the WEF system in arid and semi-arid regions.