There is a phenomenon of nutrient reduction after land leveling in Guizhou. Taking yellow soil of Guizhou province as the research object，the characteristics of microbial community and gene function in deep soil were analyzed to provide theoretical basis for rapid soil improvement after land leveling in mountainous areas. Metagenomic techniques were used to study the differences of microbial community structure and gene function in yellow soil from topsoil(0-30 cm)and deep soil(30-60 cm). The results showed that a total of 7872 species were obtained from topsoil and deep soil samples. Compared with the topsoil，the number of specific genes in deep soil increased by 64.12%，but the microbial diversity decreased by 5.36%. In terms of community composition，the relative abundance of bacteria in deep soil decreased，while the relative abundance of archaea，eukaryotes and viruses increased. At the phylum level，the relative abundance of Proteobacteria and Actinobacteria in deep soil decreased by 32.07% and 54.58%，respectively，compared with that in the topsoil layer. The relative abundance of Chloroflexi and Acidobacteria increased by 288.30% and 48.82%，respectively. The relative abundance of archaea in deep soil was 59.83% lower than that in topsoil layer. Ascomycetes in deep soil decreased by 15.90% compared with those in topsoil. Actinomycetes，Gemmatimonadetes and Thaumarchaeota of archaea were significantly enriched in the topsoil. Acidobacteria，Chlorocurvula and Firmicutes were significantly enriched in the deep soil. The abundance of functional genes of metabolic pathways in deep soil was lower than that in topsoil，and carbohydrate metabolism was the most abundant. The gene abundance of six carbohydrate active enzyme families in deep soil was lower than that in topsoil，and there were significant differences in soil glycoside hydrolase，glycosyltransferase，carbohydrate binding module and co-oxidoreductase，which decreased by 24.98%，15.46%，39.36% and 42.93% in the deep soil，respectively，compared with topsoil. The relative abundance of key genes in the carbon，nitrogen and phosphorus cycling process of korA，xylA，narZ，ureC，ppx-gppA and phoD in soil showed the same trend of decrease in the deep layer compared with the topsoil layer. In conclusion，the structure and function of microbial communities in deep soil were significantly different from those in the topsoil soil. The abundance of relevant metabolic pathway functional genes and carbohydrate active enzyme functional genes in the microbial communities gathered in deep soil reduced the nutrient cycling capacity，thus affecting the soil nutrient supply and ripening rate.