Soil acidification is causing serious harm to the ecological environment and agricultural production in southern China, but the corresponding variation of the soil microbial communities through the acidic gradient profile remains poorly investigated. Here, we investigated the soil microorganisms from normal, acid and strong acid soil samples via high-throughput sequencing technology, and described their distribution characteristics under different acidification backgrounds, and depicted their response to ambient environment factors. We found the Actinobacteriota (41.84%), Proteobacteria (27.91%), Chlorofexi (13.86%), Ascomycota (75.69%) and Basidiomycota (19.00%) composed the core microbial populations among samples. Meanwhile, Xanthobacteraceae (3.13%), Acidothermus (2.16%), Sordariomycetes (10.05%) and Thysanophora (8.71%) were more abundant in acidified soils, thus indicating a higher probability of soil borne diseases. Besides, it was found that soil acidification has more negative effects on the bacterial community, as revealed by the PICRUSt predictions that pathways of carbohydrate, lipid and protein metabolisms were seriously decreased in microbial community, however, the fungal community have a relatively stronger resistance for the acid stress since many pathways of signal transition and cell proliferation were increased abundance in the fungal community.