Tropical karst seasonal rainforests (TKSR) in southwestern China have high levels of biodiversity and a significant number of endemic species. However, understanding the distribution of plant diversity and the mechanisms driving community assembly in these diverse and heterogeneous karst forests remains limited. This study examined the species and phylogenetic diversity of the herb, shrub, and tree layers in the TKSR along steep hillslopes within karst peak-cluster depressions in southwestern China. Species richness in the herb, shrub, and tree layers showed an inverted U-shape pattern, with richness lower in the middle and higher on the sides of the hillslope. The upper slope had a higher level of species richness than the depressions and the lower and middle slopes. The phylogenetic structures of the herb and tree layers tended to be clustered, whereas the shrub layer exhibited a divergent phylogenetic structure. These findings indicate that community assembly in the TKSR is influenced by habitat filtering and competitive exclusion. Soil total phosphorus (STP) and soil available phosphorus (SAP) were identified as significant factors affecting species diversity across the three layers, whereas the rock outcrop rate was a significant factor affecting the phylogenetic structure. In the shrub and tree layers, STP and SAP were important determinants of phylogenetic diversity. These results highlight the impact of environmental heterogeneity on species and phylogenetic diversity in the TKSR. Furthermore, depressions and upper slopes with high species and phylogenetic diversity were identified as priority areas for conservation in the karst peak-cluster depressions of southwestern China.