Abstract Karst rocky desertification is a severe irreversible ecosystem failure. The karst ecosystem is so fragile that it is vulnerable to environmental changes, degrading into rocky desertification. Prior studies revealed the potential connections between the soil bacterial community, the edaphic properties and the aboveground vegetation cover in the karst ecosystem. However, how these three elements affect each other and work together in propelling in the karst rocky desertification progress largely remains unexplored. To answer this question, we monitored the bacterial community variations in soils sampled from multiple sites at a successional karst rocky desertification region by sequencing the 16S rRNA V3-V4 regions. Overall, we detected 34 bacterial phyla in the karst soils, of which Proteobacteria, Actinobacteria, and Acidobacteria are the most abundant. Network analysis of the bacterial community- vegetation-edaphic property-vegetation interactions identified 6 bacterial herds that had significant correlation with soil Ca2+ and available phosphorus change during vegetation degradation. Further functional simulation of these bacterial herds unveiled the change of Ca2+ and available phosphorus might disturb the soil carbon and nitrogen metabolism, and thus weakened soil quality. In summary, we hypothesized a calcium-driven bacterial response mechanism in the karst rocky desertification progress. Graphical abstract Unlabelled Image Highlights • The karst rocky desertification progress accompanies with the change of edaphic properties and soil microbial community structure. • The change of Ca2+ and available phosphorus in karst soils is strongly associated with six bacterial herds. • The Ca2+ and available phosphorus have close impact on the metabolism of soil carbon and nitrogen via interfering the soil bacterial community structure. [ABSTRACT FROM AUTHOR]