It is essential to protect and preserve biodiversity, especially in habitats in which natural resources are scarce. The differing flora and vegetation distribution on the broad, arid landscape at the Crown Prince Mohammed Bin Salman Nature Reserve has yet to be investigated. Based on GPS coordination and the transitional zone of plant communities, 48 symmetric plots of 50 × 50 m2 were distributed evenly over six elevations. In this study, we recorded 70 species in 33 families and elucidated floristic traits correlated with elevation. High species richness was recorded for the families Fabaceae, Poaceae, Asteraceae, and Chenopodiaceae. High numbers of chamaephyte and phanerophyte species were observed. In the chorotype, the mono-regional component contained 47% of the species, the bi-regional component 35.7%, and multi-regional and worldwide species comprised 10% and 7%, respectively. This study noted the growth habits of 23 herbs, 15 shrubs, 10 trees, and a single species of grass, vine, climber, and mistletoe. Diversity indices, indicator species, dominant plant communities, and soil profiles were compared for the defined zones of elevation. Alpha and beta diversity were high at elevations of ≥1000, 800, and ≤100 ma.s.l., compared to elevations of 600 m, 400 m, and 200 m. The highest species richness and species turnover were recorded at elevations of ≥1000, 800, and ≤100 m, while species evenness was greater at elevations of 600, 400, and 200 m. Vegetation analyses and indicator species (based on relative abundance) showed species variation with elevation. Species domination was influenced by physical soil structure and soil chemistry. Microclimates, including temperature and relative humidity variations, were found to be a significant driver in the ecosystem, resulting in varying plant diversity and species distribution at different elevations. Through canonical correspondence analysis (CCA), we used an autocorrelation of elevations, plant species, and soil properties to identify three phytogeographic categories that were presumed to be a proxy of microclimate change: Category I: elevations 1000 m and 800 m, including Retama raetam, Zilla Spinosa, and Vachellia gerrardii linked with sandy soil; Category II: elevations 600 m and 400 m, including species Haloxylon salicornicum, Rhazya stricta, and Leptadenia pyrotechnica linked with enriched soils containing CaCO3 and HCO3 and having a clay texture; and Category III: elevations 200 m and 100 m, including Zygophyllum coccineum, Tamarix nilotica, and Hyphaene thebaica, which thrived in salinity and silt soils. The spatial vegetation patterns of the xeric environment and its transition zones in Prince Mohammed Bin Salman Nature Reserve were also documented. It is recommended that microclimate effects on species nominated for vegetation restoration or afforestation be considered for the optimal management of this important nature reserve.