This study focused on soils developed from dolomite, limestone, and sand-shale parent materials in the Huajiang Research Area of Guizhou Province, using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS sequences, systematically investigated the community structures and diversities of bacteria and fungi in Zanthoxylum planispinum var. dingtanensis plantations, and their relationships with available nutrients, and differences among microbial communities in soils derived from distinct bedrock types, along with their responsiveness to soil nutrient availability. The findings aim to provide scientific support for efficient cultivation and precise management of Zanthoxylum planispinum var. dingtanensis in this region. Results showed that: 1) Lithology significantly influenced microbial community structures. Chao1 diversity index for bacteria in limestone-derived soils was significantly lower than that in dolomitic and sand-shale-derived soils (P<0.05), while Shannon and Simpson indices exhibited no significant differences across the three lithologies. 2) Ascomycota and Basidiomycota dominated the fungal phyla, whereas Actinobacteriota, Acidobacteriota, Proteobacteria, Chloroflexi, and Gemmatimonadota were dominant bacterial phyla. Sand-shale-derived soils had significantly higher relative abundance of Gemmatimonadota compared to other lithologies, while Fusarium abundance in dolomitic soils was markedly lower. 3) Redundancy analysis (RDA) revealed that fungal communities were primarily shaped by available phosphorus, whereas bacterial communities were strongly associated with pH. Principal coordinates analysis (PCoA) indicated that soil microbial communities formed distinct, non-overlapping clusters based on lithology, suggesting a strong lithological control on community structure. 4) One-way ANOVA demonstrated that limestone-derived soils contained higher levels of organic carbon, available potassium, available phosphorus, and exchangeable calcium than dolomitic and sand-shale-derived soils. Overall, these results demonstrated that variations in soil nutrient availability driven by parent material properties substantially influenced soil microbial community composition.