Subtropical forest in China has received much attention due to its complex geologic environment and bioclimatic heterogeneity. There have been very few studies addressing which climatic factors have shaped both distribution patterns and niche differentiation of species from this region. It also remains unclear whether phylogenetic niche conservatism retains in plant species from this biodiversity-rich subtropical region in China. In this study, we used geographic occurrence records and bioclimatic factors of Prunus dielsiana (Rosaceae), a wild cherry species, combined with the classical ENM-based DIVA-GIS software to access contemporary distribution and richness patterns of its natural populations. The current distribution of P. dielsiana occupied a relatively wide range but exhibited an uneven pattern eastward in general, and the core distribution zone of its populations are projected to concentrate in the Wushan and Wuling Mountain ranges of western China. Hydrothermic variables, particularly the Temperature Seasonality (bio4) are screened out quantitatively to be the most influential factors that have shaped the current geographical patterns of P. dielsiana. By comparison with other sympatric families, climatic niche at regional scale showed a pattern of phylogenetic niche conservatism within cherry species of Rosaceae. The effect of habitat filtering from altitude is more significant than those of longitude and latitude. We conclude that habitat filtering dominated by limiting hydrothermic factors is the primary driving process of the diversity pattern of P. dielsiana in subtropical China.