The Gurbantunggut Desert is the largest stable and semi-stable sand desert in China, yet few data exist on vegetation pattern and species-environment relationships for these diverse desert landscapes. The sand dunes of the survey area are mainly of the longitudinal form from north to south, but checkerboard-shaped and honeycomb-shaped forms are also present, with the height of 10–50 m. We measured vegetation and soil data on north–south transects and compared them with vegetation and soil data on east–west transects. Analysis revealed that the varying trend and strength of the species diversity, dominance and cover of the plant communities in the longitudinal and transverse directions across the landscape are significantly different. The results of CCA ordination show that the microhabitats of soil organic matter (OM), soil salts (TS), sorting index (σ), topsoil water-content (SM) and pH relate to the differences in vegetation observed as differences in species assemblage from salt-intolerant ephemerals, micro-subshrubs and subshrubs to salt-tolerant shrubs and micro-arbors. The terrain (alt.) and soil texture (the contents of Mz and φ1) affect the spatial differentiation of many species. However, this spatial differentiation is not so marked on transects running longitudinally with the landscape, in the same direction as the dunes. The species of the desert vegetation have formed three assemblages under the action of habitat gradients, relating to three sections running transversely across the landscape, at right angles to the direction of the dune crests. In the mid-east section of the study area the topography is higher, with sand-lands or dune-slopes with coarse particles. Here the dominant vegetation comprises shrubs and subshrubs of Seriphidium santolium and Ephedra distachya, with large numbers of ephemeral and ephemeroid plants of Senecio subdentatus, and Carex physodes in spring and summer. On the soil of the dune-slopes in the mid-west of the study area, with coarse particles and abundant TK, the plant assemblage of Haloxylon persicum, Soranthus meyeri and Agriophyllum squarrosum is developed. The species composition in the east marginal belt of the study area has similar characteristics to the mid-west section. There is no corresponding section in the north–south transects (except for the north and south margins). This is because the habitats of most plants are located in the middle of the microhabitat gradients in the north–south direction in the desert.