It is known that soils derived from different parent materials drive the distinct bacterial community structures, however, the influence of soils derived from the same soil parent material in different development stages of karst on the microbial diversity are unknown. In this study, three calcareous soils (including yellow, red and black calcareous soils) derived from different development stages in karst shrub ecosystems were collected at five profile layers up to 100 cm deep, and were determined bacterial communities by using Illumina amplicon sequencing and quantitative polymerase chain reaction (qPCR) techniques. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Verrucomicrobia dominated the calcareous soils from karst shrub ecosystems. The relative abundances of Proteobacteria and Firmicutes increased with the increasing profile depth in three calcareous soils, while Acidobacteria and Verrucomicrobia were opposite. The diversities of bacterial communities in topsoil layers at 0~40 cm depths were higher than those of layers below 40 cm deep, but became similar at depths below 40 cm. The bacterial community structures differed among three calcareous soils, and were different between the surface layers and the other layers in all soils. The abundance and structure of bacteria was strongly related to soil organic carbon, suggesting their importance for carbon cycle. Path analysis showed that soil bacterial community structure can be directly influenced by calcareous soil type, and indirectly impacted by soil depths through soil properties. Our findings revealed that calcareous soil type was an important factor in determining soil bacterial community structure, and bacterial succession was closely related to the formation of calcareous soil in karst regions.