The distribution of plant diversity is influenced by the environment, such that one area is species-rich, another area species-poor and intermediate areas of moderate richness, so it is scale-dependent, so it is scale-dependent. Studying the variety and distributed regularity of plant diversity in different regions can help us understand the underlying reasons for plant community diversity and changes to this diversity, and determine how to effectively protect and use these plant resources. In this study, we focused on the south Gurbantonggut desert, a known center of plant diversity. We divided the study site along the meridional direction into the following three transects:the oasis edge, the desert highroad from Karamay to Jimusaer, and the desert hinterland. We also divided the study site into five regions, according to the height and trend of dunes and differences in habitats. We analyzed the α-diversity and β-diversity in all transects and regions, and summarized the similarities and differences in species composition. These results showed that the α-diversity in the three transects differed, with the order as follows:oasis edge transect > desert highway transect > desert hinterland transect. The β-diversity (species similarity and substitution) of the transects varied similarly with increasing longitude. According to the species composition analysis, the desert highway transect consisted mostly of ephemeral plants, the oasis edge transect had mostly perennial herbs and shrubs, and the diversity in the desert hinterland transect had a mix of ephemeral plants, perennial herbs, and shrubs. We also observed a difference in species composition among the regions. Species richness in the western part of the desert, the Mosuowan reclamation area, desert interior, and the eastern part of the desert was high, whereas that of the Manasi Lake area was relatively low. Although species similarity of the Manasi Lake was low, its species substitution rate was high, when compared with other regions. We concluded that plant diversity among the regions is driven by the geological processes of the species pool, and that plant diversity among the transects is driven by environmental factors such as soil texture and precipitation. The eastern part of the study area was determined to be the species diffusion center of the south Gurbantonggut desert.