Desert plant communities play a crucial role in enhancing desert ecosystem productivity and stability but are highly susceptible to environmental changes owing to their limited resilience and resistance to disturbances, making it essential to understand the factors influencing their diversity patterns and community structure, particularly under the threat of climate change and intensifying droughts. This study focused on the Turpan-Hami desert region, a typical desert ecosystem in which diversity patterns and community structures remain unclear. We established 101 sampling sites ranging from elevations of -134 to 2056m and recorded community information, including species composition, height, coverage, and density, using the sample plot method. The diversity patterns were analyzed using regression analysis, and the phylogenetic structure was assessed. Additionally, Canonical Correspondence Analysis, Mantel tests, and General Linear Models were used to identify the key factors affecting community structure. Our results demonstrated that the species richness and phylogenetic diversity of plant communities exhibited a monotonic increase with elevation, and the phylogenetic structure exhibited low clustering and high dispersion along the elevational gradient. The annual mean temperature emerged as the most significant factor influencing diversity patterns, with soil nutrients, such as total potassium and available phosphorus, also affecting the spatial distribution of diversity. Notably, no significant correlations were found between community phylogenetic structure and abiotic factors, highlighting the complex interactions that drive diversity in the Turpan-Hami region. This study offers valuable insights into the mechanisms shaping desert plant community diversity and is essential for biodiversity conservation efforts in fragile desert ecosystems amid climate change.