Bacterial communities play key roles in maintaining ecosystem multifunctionality. With increasing land use intensity, soil biogeochemical and microbial characteristics change significantly and may affect the multifunctionality of ecosystems. The relationship between soil microbial communities and resistance of multiple ecosystem functions under land-use change has not previously been assessed in the karst regions. Soils from four karst ecosystems (primary forest, secondary forest, abandoned land and cultivated land) were analyzed for microbial communities as predictor of multifunctional resistance to land use change by using high-throughput sequencing, structural equation modeling and random forest modeling. We evaluated the multifunctional resistance of soil ecosystems by measuring indicators related to soil carbon, nitrogen and phosphorus cycling. The resistance of Proteobacteria was the highest in the secondary forest, and that of Verrucomicrobia was the highest in the abandoned and cultivated lands. With increasing land-use intensity, C-cycling functional resistance decreased by 77% and nitrogen functional resistance increased by 17% in the abandoned land, compared with those in the secondary forest. Bacterial communities had the largest direct positive effect on multifunctional resistance and N-related functional resistance. Among bacterial communities, Verrucomicrobia and Chloroflexi were the two most important phyla that affected soil multifunctional resistance. Armatimonadetes_unclassified, Chloroflexia and OPB35_soil_group were the best predictor of total organic carbon, total nitrogen and total phosphorus content, respectively. Our results suggested strong links between microbial community composition and multifunctional resistance in various karst ecosystems, and provided insights into the importance of microbial community composition in the recovery of ecosystems following human intervention.