Aims <p>This study aims to investigate the interrelationships among vegetation, soil biota, and environmental factors in the karst rocky desertification (KRD) ecosystem, with the objective of elucidating the maintenance and stability of this ecological process.</p> Methods <p>Large-scale vegetation surveys were conducted across four KRD grades. Data on plants, soil fauna, microorganisms, and soil physicochemical properties were collected. Biodiversity, co-occurrence networks, and plant-soil biota-environment interactions were quantified using principal component analysis and partial least squares structural equation modeling.</p> Results <p>During rocky desertification succession, plant communities transition from tree to herb dominance, accompanied by declines in plant α-diversity and FEve. Soil fauna diversity follows a pattern of initial decrease followed by recovery, with protozoa being the most responsive group. Fungal diversity declines consistently, whereas bacterial diversity decreases initially but exhibits functional compensation through species replacement. The plant-soil biodiversity network shifts from early-stage isolation to later weak mutualism and functional synergy, manifested by negative protozoa-bacteria correlations, strengthened fungi-plant positive relationships, and a transition to bacterial-fungal cooperation. Diversity variations are jointly driven by soil “structure-water-nutrient” and “pH-Si/TOC” gradients, with moisture content, nitrogen/phosphorus nutrients, and carbon-silicon stoichiometry as core factors. Further analysis reveals direct suppression of plant and fungal diversity by rocky desertification, while plant diversity indirectly enhances microbial diversity by improving soil physicochemical properties.</p> Conclusions <p>These interactions reveal a nutrient-driven “positive feedback degradation cycle” in KRD ecosystems. Our findings provide critical theoretical support for guiding ecological restoration efforts in karst regions.</p>