In order to build a good arable layer of mountainous tobacco plating soil，a field experiments were conducted in the alkaline tobacco-growing area of Baoshan to study the response characteristics of soil microbial community to deep tillage and incorporated bio-organic fertilizer.Randomized field trials were conducted with deep tillage (30 cm) as the main treatment and different doses of bio-organic fertilizer as the secondary treatment.Soil physical and chemical properties，microbial abundance and diversity，community structure characteristics and functional groups of each treatment were tested and analyzed using general test methods and Illumina MiSeq sequencing techniques，respectively.Finally，the improvement effects of deep tillage and incorporated bio-organic fertilizer on alkaline tobacco-planting soil quality were discussed.The results of diversity analysis showed that there was no significant difference in Chao index and Shannon index of microbial community under the treatment of deep tillage and incorporated bio-organic fertilizer，but the difference of microbial community，especially fungal community，was enhanced.Compared with those of before cultivation，the abundance of Proteobacteria，Acidobacteria，Mortierellomycota and Basidiomycota increased significantly，while the abundance of Actinobacteria and Ascomycota were decreased significantly under chemical fertilizer treatment.In addition，the abundance of Proteobacteria and Mortierellomycota increased significantly，while the abundance of Chloroflexi，Acidobacteria and Basidiomycota decreased significantly under bio-organic fertilizer treatment.Compared with chemical fertilizer treatment，the abundance of Actinobacteria，Proteobacteri and Ascomycot populations increased significantly，while the abundance of Chloroflexi，Acidobacteria and Basidiomycot decreased significantly under bio-organic fertilizer treatment.The results of BugBase phenotypic prediction and FUNGuild functional prediction showed that the abundance of pathogenic bacteria and fungi decreased significantly，and the abundance of soil microbial functional groups increased significantly.Correlation analysis showed that soil bulk density and organic matter were the main physical and chemical factors affecting soil microbial community structure.Deep tillage and incorporated bio-organic fertilizer could regulate the composition of soil bacterial and fungal community structure by improving soil physical and chemical properties，increase the abundance of beneficial microbial population，and reduce the abundance of pathogenic bacteria.