The degradation of karst ecosystem in Southwest China has been a serious ecological problem. To research the effects of different vegetation types on microbial biomass and bacterial community structures of rhizosphere soil, we selected the dominant tree species, Quercus fabri, Platycarya longipes in forest and Pyracantha fortuneana, Zanthoxylum planispinum in shrubbery, in two typical karst ecosystems. The results showed that microbial biomass carbon and nitrogen of rhizosphere soil in forest were higher than those in shrubbery, and the effects of the dominant tree species of Quercus fabri and Platycarya longipes in forest was more obvious compared to shrubbery. Bacterial diversity indexes of rhizosphere soil of dominant tree species in forest were significantly higher than those of bulk soil by the root exudates, but in shrubbery, there was no significant difference in both microbial biomass and diversity indexes between rhizosphere soil and bulk soil. It suggests that the vegetation succession could affect the cycle of substance and energy among plant-microbe-soil system by changing the characters of soil microbe, even affect the stabilization and health of karst ecosystems.