Abstract: This study collected soil samples from Hani terraced fields under the traditional farming methods, and from naturally occurring forest soils, which were avoid of influence by artificial rice-growing cultivation using 16S rRNA high-throughput sequencing technologies. We then compared soil microbial taxonomical and functional similarities and differences between these samples, as to reflect the natural responsive characteristics of the soil microorganisms to anthropogenic disturbance. The results showed that the Alpha diversity of paddy soil microorganisms was significantly higher than that of forest soil, and there were significant differences in microbial community structure between 2 soil types. At the phylum level, the dominant bacteria in paddy soil are Chloroflexi and Bacteroidetes, while the dominant bacteria in forest soil are Actinobacteria and Planctomycetes; microbial differences between soil types are even more obvious at the genus level. As seen, Geobacter was the dominant bacteria in paddy soil, while Anaeromyxobacter was the dominant bacteria in forest soil. The differential analysis revealed that Geobacter could be used as a biomarker indicator of microbial communities in paddy soil, while Bradyrhizobium is the microbial biomarker in forest soil. Canonical correspondence analysis showed that the main environmental factor affecting the microbial communities in paddy soil was flooding depth. Microbial functional analysis found that the main function of microbial communities in paddy soil were related to iron respiration respiration of sulfur compounds and oxidation by aerobic nitrite. In contrast, main functions of forest soil microbial communities were those associated with cellulolysis and aromatic compound degradation. Such functional differences between 2 soil types were remarkably significant, indicating that in conventional tillage conditions, affected by rice flooded-drying alternation, iron respiration and nutrient element cycling in paddy soil microbiota have been greatly enhanced. The traditional tillage method will significantly change soil microbial community structure and functional characteristics, and significantly improve microbial diversity. The study provides an important reference for further revealing the evolution of soil ecological functions under traditional tillage.