Nutrients are vital for plant subsistence and growth in nutrient-poor and arid ecosystems. The deep roots of phreatophytic plants are necessary to access groundwater, which is the major source of nutrients for phreatophytes in an arid desert ecosystem. However, the mechanisms through which changes in groundwater depth affect nutrient cycles of phreatophytic plants are still poorly understood. This study was performed to reveal the adaptive strategies involving the nutrient use efficiency (NUE) and nutrient resorption efficiency (NRE) of desert phreatophytes as affected by different groundwater depths. This work investigated the nitrogen (N), phosphorus (P), and potassium (K) concentrations in leaf, stem, and assimilating branch, as well as the NUE and NRE of the phreatophytic Alhagi sparsifolia. The plant was grown at groundwater depths of 2.5, 4.5, and 11.0 m during 2015 and 2016 in a desert-oasis transition ecotone at the southern rim of the Taklimakan Desert in northwestern China. Results show that the leaf, stem, and assimilating branch P concentrations of A. sparsifolia at 4.5 m groundwater depth were significantly lower than those at 2.5 and 11.0 m groundwater depths. The K concentrations in different tissues of A. sparsifolia at 4.5 m groundwater depth were significantly higher than those at 2.5 and 11.0 m groundwater depths. Conversely, the NRE of P in A. sparsifolia was the highest among the three groundwater depths, while that of K in A. sparsifolia was the lowest among the three groundwater depths in 2015 and 2016. The N concentration and NUE of N, P, and K in A. sparsifolia, however, were not influenced by groundwater depth. Further analyses using structural equation models showed that groundwater depth had significant effects on the P and K resorption of A. sparsifolia by changing soil P and senescent leaf K concentrations. Overall, our results suggest groundwater depths affect P and K concentrations and resorption but not their utilization in a desert phreatophyte in its hyper-arid environment. This study provides a new insight into the phreatophytic plant nutrient cycle strategy under a changing external environment in a hyper-arid ecosystem.