To explore the changes of microbial community structure in tobacco-planting soil after application of silicon-rich soil improvement fertilizer and the effects of functional flora on soil nutrients and yield and quality of flue-cured tobacco, the root soil of flue-cured tobacco variety ‘K326’ was used as the experimental material, and the silicon fertilizer of 75 kg/hm² was supplemented under the condition of conventional application of organic fertilizer as the base fertilizer, and the local conventional fertilization scheme was used as the control. By recording the agronomic traits of tobacco plants in the field and the economic traits of tobacco leaves, the Illumina Mi Seq high-throughput sequencing was used to measure the fungi, bacteria genes and conventional physical and chemical properties of tobacco root soil in the two treatments. The results showed that the soil available phosphorus, organic matter content and pH, agronomic traits of tobacco plants and economic traits of flue-cured tobacco leaves treated with silicon-rich soil improvement fertilizer were significantly higher than those of the control treatment. There was no significant difference in the classification level of fungi and bacteria between the two treatments. Ascomycota, Basidiomycota, Actinobacteriota, Proteobacteria and Firmicutes were the main fungi and bacteria. At the genus level, Fusarium, Saitozyma, Chaetomium and Sphingomonas were the dominant genera in the silicon-rich soil improvement fertilizer treatment, and unclassified_k__Fungi was the unique genus in this treatment. Among them, Chaetomium, Saitozyma, unclassified_c__Sordariomycetes, Bradyrhizobium and norank_f_JG30-KF-AS9 showed a significant positive correlation with soil nutrients. Effective nitrogen content and pH were greatly affected by fungal microorganisms, and organic matter was greatly affected by bacterial microorganisms. The richness of fungal species in the root soil of tobacco plants treated with silicon-rich soil improvement fertilizer was lower than that of the control treatment, and saprotroph fungi were the main fungal types. The bacterial species richness and KO number were significantly higher than those of the control treatment. The results showed that the application of silicon-rich soil improved fertilizer could not only increase the yield and output value of flue-cured tobacco, but also supplement soil fertility and regulate soil acidity, and slow down the acidification degree of sandy soil. In this study, the effects of soil improvement fertilizer on acidified sandy soil in high altitude area were compared from the perspective of soil microbial structure and function prediction, in order to provide scientific reference for the scientific and reasonable application of agricultural production fertilizer and the production of microbial fertilizer in similar areas.