The objective of this study was to explore the effects of longterm organic and inorganic on the structure and function of microbial community in red soil.Soil samples were collected from 4 treatments（ieCK：no fertilizer treatment；M：organic manure treatment；NPK：chemical fertilizer treatment and NPKM：combination of organic and chemical fertilizers treatment）in Qiyang Longterm Fertilization Experiment Station.Structure and abundance of bacterial and fungi communities were analyzed with Ion Torrent and realtime quantitative PCR（qPCR），respectively.Microbial respiration，soil enzymes and soil properties were also measured.Results showed that longterm application of fertilizer changed soil pH and soil properties.Application of organic fertilizers（M and NPKM）increased abundance and diversity of bacterial and fungi communities，while chemical fertilizer just increased abundance and diversity of fungi community.Longterm application of fertilizers significantly changed the structure of bacterial and fungi communities.Microbial respiration，cellobiohydrolase and phenol oxidase were significantly correlated with the structure of bacterial community but not with that of fungi community.In conclusion，application of organic fertilizer could not only alleviate the soil acidification，but also support more abundant and diverse microbial populations and consequently maintain the higher soil activity and soil fertility.