Spatial heterogeneity is considered as a ubiquitous feature in natural ecosystems. It is also well known that soil heterogeneity is a basic element for competitive and/or facilitative for resources competitive and interactions between plants, especially in the stressed environments of arid shrub-desert and steppe ecosystems. Consequently, soil spatial heterogeneity may determine the occurrence of plants, structure of vegetation and pattern of landscapes, and greatly affect biogeochemical cycles. At the regional or landscape scale, climatic and geomorphologic factors often exert strong influences on the soil spatial heterogeneity, however, local-scaled topography and vegetation should not be ignored because they are important factors in the formation of small-scaled landscape patterns. This study was designed to investigate the spatial pattern of soil water and chemical properties and their relationship in Gurbantunggut Desert ranged from the south fringe to the hinterland of about 25 km. The results showed that soil water and soil chemical properties presented a decreasing trend from the south fringe to the hinterland at the interdune, especially at about 10 km away from the south fringe, e.g., a significant peak value was appeared at the distance of 6-7 km away from the fringe. However, it was a fluctuated pattern at the slope and top dune; it indicated that climatic and geomorphologic factors exerted strong influences on the spatial heterogeneity of soil at the interdune, but not on the slope and top dune. This phenomenon can be explained as the significant decreasing of groundwater level and precipitation from the south fringe to the hinterland. In addition, soil water and chemical properties were significantly higher at the interdune than they were at the slope and the top dune, since the local topographic conditions resulted in water and soil accumulating significantly at the interdune compared to the slop and the top dune. Furthermore, soil water and chemical properties at different soil depth were significantly different, soil water content, pH and electrical conductivity increased with the soil depth, while soil nutrients content decreased with the soil depth. It indicated soil salinity and soil nutrient status behaved differently in spatial heterogeneity, with an inverse distribution between soil nutrients and soil salinity/alkalinity at different soil depth. Correlation analysis also confirmed that soil water and chemical properties were significantly correlated at the interdune in April, May and annual averaged period. It further documented that climatic and geomorphologic factors exert strong influences on the spatial heterogeneity of soil, especially since topography is the most important factor for the spatial pattern in soil properties at Gurbantunggut Desert, which lead to soil water and soil recourses accumulated significantly at the interdune in April and May. In summary, our results showed that within a population or community and over tens of kilometers, soil spatial heterogeneity was caused by climatic, geomorphologic (abiotic) and dominant plant types (biotic) together. However, these biotic and abiotic factors were not absolutely separated, but inter-linked each other, i.e., plant-soil interactions. The spatial heterogeneity of abiotic factors determined the spatial patterning of biotic factor, conversely, spatial patterns of plant distribution influenced rates of soil physical and biogeochemical processes.