Soil multifunctionality (SMF) is considered as a key ecological function indicators in the nutrient cycling process of terrestrial ecosystems. However, the effect of elevation on the SMF in a typical arid region and the driving factors remains unclear. Here, soil samples were collected from the Junggar Desert in 2022 to determine nutrient content and measure associated environmental variables. The nonlinear regression, ordinary least squares (OLS) regression, principal component analysis (PCA), and random forest (RF) model were used to assess the impact of environmental factors on SMF along an elevational gradient. The results revealed that the SMF of soils exhibits a trend of increasing first and then decreasing with increasing of elevation in the Junggar Desert ecosystem, withSa critical thresholdSobserved at 520 m. A strong positive correlation was found between SMF and net primary productivity (NPP) at elevations below 520 m, whereas no significant relationship was observed above this elevation. According to the RF model, mean annual precipitation (MAP) showed the highest relative importance in influencing SMF at elevations below 520 m, while electrical conductivity (EC) had the lowest. Conversely, pH had the greatest relative importance on SMF, and soil water content (SWC) the least, at elevations above 520 m. Briefly, the SMF in Junggar Desert was controlled by the MAP along an elevational gradient. Notably, Low-altitude (below 520 m) was regulated by NPP, while high-altitude (above 520 m) was regulated by soil pH. These findings provide a scientific basis for the conservation and restoration of typical arid ecosystems and suggest science-based strategies for soil resource management in arid regions.