Transition zones between riparian and desert ecosystems are critical sentinels of environmental change, yet how microbial metabolic plasticity and resource use trade-offs respond to these steep environmental gradients remains poorly understood. This study investigated the transition zone along the Aqikesu River in the Ebinur Lake Wetland National Nature Reserve (ELWNNR), Xinjiang. By analyzing soil extracellular enzyme activities and stoichiometric characteristics across three habitats-mesic riparian (MR), arid desert (AD), and desert erosion (DE) areas, we explored the adaptive strategies of microbial metabolic limitation patterns and potential nutrient use efficiency, along with their driving mechanisms. Results revealed significant divergence in microbial nutrient limitations along the environmental gradient: the MR exhibited higher activities of carbon-acquisition enzymes and nitrogen-acquisition enzymes, while vector analysis indicated a relatively stronger carbon limitation in this area. The DE showed elevated phosphorus-acquisition enzyme activity with alleviated nitrogen limitation. Enzyme stoichiometric vector analysis demonstrated that nitrogen limitation dominated across the entire region, but carbon limitation was more pronounced in the MR area, while nitrogen limitation was mitigated in the DE area. Microbial carbon use efficiency (CUE) increased with increasing distance from the riverbank, whereas nitrogen use efficiency (NUE) declined. The random forest (RF) analysis identified litter nutrients, soil physicochemical properties, and the relative abundance of Acidobacteriota as the primary predictors of metabolic shifts. Partial least squares path modeling (PLS-PM) further elucidated the hierarchical regulatory pathways, revealing that abiotic constraints indirectly modulated CUE and NUE by driving shifts in microbial biomass and community diversity. These findings indicate that microbial nutrient use strategies are coregulated by environmental stressors and biological attributes, reflecting a distinct metabolic trade-off along the riparianto-desert gradient. This study demonstrates the transition from growth-dominance to survival-dominance strategies in desert microbes and provides a theoretical basis for understanding the vulnerability and resilience of desert ecosystems under global desertification.