To understand the change and distinction of the top-soil microbial community structure and its diversity, three natural secondary forests (Davidii-Betula platyphylla-B.albosinensis broad-leaved forest, ABB; Betula platyphylla-Acer davidii-Abies faxoniana mixed coniferous and broad-leaved forest, BAA; Abies faxoniana forest, AFF) were investigated based on the background of similar microclimate and soil parent materials in Miyaluo forest area of western Sichuan, where the forests formed by natural regeneration after logging in the 1960s.Chemical properties of soil and species diversity of plant community were analyzed. We used high-throughput sequencing of top-soil DNA to analyze soil bacterial and fungal community composition. The results implied that the forest types significantly changed the soil microbial community composition. The Shannon index of soil fungi communities differed dramatically among the three natural secondary forests, but had no significant differences in soil bacterial communities. Furthermore, Chao1 and Shannon index of soil bacteria were significantly higher than those of fungi. Proteobacteria, Acidobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi were the dominant phyla among three secondary forests, accounting for more than 82%. Ascomycota and Basidiomycota of fungal communityaccounted for over 85%. Redundancy analysis results showed that soil pH and Shannon index of tree layer were the main factors governing soil bacterial and fungal community structure, while soil TN(Total nitrogen) and TP(Total phosphorus) contents largely explained the shift in the fungal community structure. In general, our results provide insights into the importance of species composition of tree layer, soil acidity, TN and TP content in affecting soil microbial community composition and diversity, while providing reference for the mechanisms of carbon and nitrogen sequestration and soil microbial diversity in natural secondary forest resource management and conservation.