Multi-orientation diagnosing the relationship development status of the water-food-ecology (WFE) nexus, as well as exploring threshold effects of key influencing factors, are crucial for promoting the formulation of targeted high-quality development management policies. In most studies, however, there is a lack of in-depth exploration in the impact threshold and asynchronous evolution mechanisms of the WFE nexus. To make up for these research shortcomings, this study proposes a five-dimensional (synergy-sustainability-security-efficiency-risk) assessment framework and the influencing mechanism analysis framework (endogenous constraints-exogenous disturbances-threshold effects). Results showed that (1) Throughout the research period, although the synergy and security of the WFE nexus improved slightly, the sustainability and efficiency remained inadequate, and spatial imbalances were evident. (2) The WFE nexus was prone to catastrophic and severe risks, especially one-dimensional risk, and two-dimensional composite risk for reliability-risk resistance. (3) Environmental pollution and resource pressure caused by food production were the main internal limiting factors, while GDP, DEM, and P were the primary external influencing factors. Further, these impacts increasingly played a decisive role. (4) There were optimal thresholds for the impact of key internal and external influencing factors towards the development of the WFE nexus. The results emphasize the intricate interconnections among water, food, and ecology and excavate optimal thresholds for the dominant factors of the WFE nexus, which can offer insights for the implementation of the WFE nexus-related management measures to promote sustainable development of Arid Northwest China.