The study was designed to study spatial variation of soil pH, electrical conductivity, soil organic carbon, total nitrogen, available nitrogen, total phosphorus and available phosphorus, and scale characteristics of spatial heterogeneity of the soil chemical properties at various scales, such as rhizosphere, individual, population, topography and region, separately in the Gurbantunggut Desert, with the purpose of finding out at which scale the heterogeneity was the greatest and its dominating factor. Results show that soil pH demonstrating an order of individual > population > topography > region > rhizosphere, which indicated that the variation of soil pH in the desert ecosystem was dominated by the biotic progress of plant individual and population. The effects of topography, climate and hydraulics were very limited, and the effect of rhizosphere was the least. In terms of electrical conductivity, the scales followed the order of individual > region > population > topography > rhizosphere, which demonstrated that an individual of shrub played a dominating role in variation of soil salt around the taproot. For soil organic carbon, total nitrogen, available nitrogen and available phosphorus, the highest heterogeneity also existed at the individual scale, which was followed by the topography scale, and the least did at the population scale, which suggested shrub individuals were the factor dominating soil nutrients, topography was the next, and population was the least. For soil total phosphorus, heterogeneity was the highest at the scale of topography and the smallest at the scale of rhizosphere, indicating topography and plant individual were the major factors affecting heterogeneity of soil total phosphorus, and the rhizosphere was the least.