Despite the numerous studies on the large-scale patterns of species richness, the spatial variation and determinants of species richness for the alpine plants are still an outstanding question and critical to future biodiversity conservation. The genusSaxifragais a typical alpine plant group with high species richness in the Himalaya-Hengduan Mountain (HHM) regions, China. We performed simple regression models and variance partitioning to assess the importance of different factors, especially soil-related ones, in drivingSaxifragarichness patterns. The results showed that environmental energy, habitat heterogeneity, and soil heterogeneity together dominated the spatial variation of species richness. The coarse fragment volume (CRFVOL) of soil, elevation range, and soil heterogeneity are positively related toSaxifragarichness. Soil slightly outperforms habitat heterogeneity in predicting the spatial variation ofSaxifragaspecies richness with an explanatory power of 39.3% and 36.6%, respectively. Environmental energy, such as the maximum temperature of the warmest quarter, is negatively correlated with species richness and explains 44.8% of spatial variation ofSaxifragarichness. Multiple regression models, including three variables, each representing energy, soil, and habitat heterogeneity, can only explain 53.1% variation of species richness. Variance partitioning outscored 26% of the shared effects of the three variables, while the independent effect of each variable is less than 10%. These results indicated that the energy, soil, and habitat heterogeneity together are primary determinants of the spatial variation ofSaxifragaspecies richness. However, there are probably other hidden factors predicting species richness variation due to the low explanatory power of the multiple regression models. Our study emphasizes the significance of soil properties in determining species richness patterns in China, especially for alpine plant groups. The negative association of species richness with temperature suggests a potential threat of alpine biodiversity loss in HHM from future warming.