Although Artemisia ordosica Krasch. and Sabina vulgaris Ant. are the dominant shrub species in the Mu-us desert ecosystem, they differ in their botanical traits. We investigated the spatial patterns of soil properties using geostatistical analysis to examine the effect of plant species on these spatial patterns. Comparison among three microsite types (under A. ordosica, under S. vulgaris, and the opening between vegetation) showed that A. ordosica generally had less effect than S. vulgaris on local soil properties. The long life-span, prostrate life-form, and evergreen leaf-habit of S. vulgaris may lead to a higher accumulation of organic and fine materials under S. vulgaris. The range of spatial autocorrelation found in the mass of organic matter on the soil surface was smaller than that of the coverage of S. vulgaris (11.5 m) which corresponded to the canopy patch size of this species, and was longer than the canopy patch size of A. ordosica. The ranges of total C and N, and pH (11.7–15.6 m) were similar to that of S. vulgaris. The range of available P (106.3 m) was comparable to that of the coverage of A. ordosica (86.2 m) considered to be the scale of the distribution of this species. The ranges of silt+clay and exchangeable K, Ca, and Mg (31.0–46.7 m) were not related to plant presence, and were similar to that of topography (43.1 m).