Soil microbial communities change along the soil depth，and information on the dynamics of soil microbial community profiles is valuable for predicting the long-term activities of soil microbial communities in rice fields in karst regions at various soil diagnostic layers. The effects of changes in soil depth on soil microbial communities in paddy fields in karst areas were investigated using high-throughput sequencing of 16S rRNA and ITS amplicons. The results indicated that changes in soil depth significantly affected soil enzyme activity and altered the composition and microbial diversity of bacterial and fungal communities. A total of 61 bacterial phyla and 18 fungal phyla were identified. The dominant bacterial phyla in the soil were Acidobacteriota(relative abundance of 22.54%)，Chloroflexi(relative abundance of 16.67%)，and Proteobacteria(relative abundance of 16.58%). In deeper soil layers，the relative abundance of eutrophic bacteria was lower(Proteobacteria decreased from 20.10% in surface soil to 16.04% in deeper soil)，while the relative abundance of oligotrophic bacteria was higher(Acidobacteriota increased from 20.27% in surface soil to 26.88% in deeper soil). The dominant fungal phyla included Ascomycota(relative abundance of 43.22%)and Basidiomycota(relative abundance of 21.04%). Alkali-hydrolyzable nitrogen and acid phosphatase enzyme were significant drivers of bacterial communities(R2 = 0.5391 and 0.5085，respectively，P<0.001)，while sucrase and available phosphorus were key drivers of fungal communities(R2=0.2577 and 0.2032，respectively，P<0.05). Compared to fungal communities，bacterial communities showed a stronger correlation with environmental factors. As soil depth increased，physicochemical indicators exhibited a declining trend. Soil microbial diversity and co-occurrence networks initially decreased and then increased with soil depth. The surface soil microbial network comprised 324 nodes and 754 edges，showing a declining trend with depth，but increased again to 79 nodes and 94 edges in the deeper soil. This study provided new insights into the changes in soil microbial communities with soil depth in paddy fields in karst regions.