Sequencing of the metagenome was used to comparatively analyze the composition and the diversity of microbial communities in soil under the four fertilizations including no fertilization （CK）， nitrogen， phosphorus and potassium fertilizers （NPK）， organic fertilizer （OM）， and organic fertilizer mixed with nitrogen， phosphorus and potassium fertilizers （NPKOM） in experiments of long-term positioning to study the relationship between the microbial communities in dryland red soils and the systems of fertilization. The results showed that OM and NPKOM significantly increased the abundance of Actinobacteria and Proteobacteria compared to CK， but decreased the abundance of Chloroflexi. Fertilization significantly changed the structure of microbial community in soil， with OM reducing and NPKOM increasing the number of microorganisms in soil. The microbial community in soil was significantly correlated with pH and the content of total phosphorus （TP）， soil organic matter （SOM）， alkali-hydrolyzable nitrogen （AN）， and available phosphorus （AP） at the level of phylum. pH was a key factor affecting the structure of microbial communities in soil. There were significant differences in metabolic functions of microorganisms under different fertilizations. It will provide a certain theoretical basis for the rational fertilization in dryland red soils in China.