Understanding the mechanism of species coexistence remains a prominent topic in ecology, particularly those unique ecosystems. Karst forests, shaped by distinctive geological and hydrological conditions, are characterized by fragile structures and hyper-diverse species assemblages due to water scarcity and habitat heterogeneity. The effects of limited water resources on forest structure and species diversity were investigated across 20 plots in the Maolan Natural Reserve. Water use efficiency (WUE) was quantified using isotopic approaches for keystone species. Significant differences in WUE were observed between evergreen and deciduous keystone species. Topographic factors predominantly influenced the WUE of evergreen species, while soil nutrients were the primary drivers for deciduous species. Additionally, topography impacted species diversity through modifications in the WUE of evergreen species and niche overlap, whereas soil nutrients primarily influenced the stand spatial structure. The results highlight the pivotal role of evergreen species in maintaining the structural stability of evergreen-deciduous mixed forests under resource constraints.