Desertification poses a permanent threat to the security of arid ecosystems. Perennial arid vegetation plays a crucial role in maintaining the structure and function of arid ecosystems and slowing the process of desertification by forming “fertile islands” under the tree canopy. However, the process of formation and development of these fertile islands remains uncertain. Here, we explored how three typical woody plants (i.e., Populus euphratica, Haloxylon ammodendron, and Nitraria tangutorum) in the Ebinur Lake Basin of northwestern China differed in their soil nitrogen and phosphorus. 1) Significant differences of organic carbon and total and available nitrogen/phosphorus were observed in the soil among the three typical woody plant-dominated ecosystems. Populus euphratica had significant differences of N and P contents between the canopy and bare soils, except for ammonium nitrogen. 2) Our RDA analysis revealed that the major factors that influenced the soil nutrient differences among the three vegetations were plant crown width, soil water content, salinity, and pH. 3) The organic carbon content of bare soil was significantly correlated with N and P in all the three vegetations. This study contributes to our understanding of the factors that influence the fertile island effect in arid ecosystems, which may contribute to soil conservation in arid areas.