Soil microbes are a crucial component of karst ecosystems, and exploring their community changes during succession can help to elucidate the mechanisms driving succession dynamics. However, the variation of soil microbial communities during vegetation succession in karst ecosystems is still poorly understood. We studied the variations in community structure and potential functions of soil microbes within the four successional stages of grassland (GL), shrubland (SL), secondary forest (SF), and primary forest (PF) for the topsoil (0–10 cm) and subsoil (10–20 cm) in a karst area using high-throughput sequencing. The research findings showed that the bacterial and fungal community diversity and composition changed more obviously in the topsoil than in the subsoil across the succession. With vegetation succession, the structural and functional characteristics of soil bacterial and fungal communities show different trends, with soil fungal communities having a greater response to successional stage changes. Actinobacteria and Acidobacteria were dominant in secondary and primary forests, respectively, while Bacteroidetes was prevalent in grassland. However, the change in Proteobacteria was not significant at both soil depths. Ascomycota was the dominant phylum of soil fungi throughout the succession. The function of soil bacteria was mainly carbohydrate metabolism, which had the highest proportion in the shrubland at different soil depths. The dominant fungal functional groups were saprotroph, pathotroph, and pathotroph–saprotroph. The soil bacterial communities were observably affected by soil organic carbon, total nitrogen, total potassium, ammonia nitrogen, nitrate nitrogen, and leucine aminopeptidase, among which soil organic carbon, ammonia nitrogen, and leucine aminopeptidase mainly influenced the bacterial community in the topsoil, while nitrate nitrogen chiefly influenced the bacterial community in the subsoil. The soil fungal community was only significantly affected by soil organic carbon. Collectively, these results indicate that the effects of vegetation succession on soil microbial communities are largely driven by successional stage and soil properties, with soil fungi being more susceptible to the vegetation successional stage and soil bacteria being more sensitive to the soil properties. During this process, soil bacterial and fungal communities follow different succession patterns.