Silicon (Si) is widely used in improving crop yield, but effect of its application on soil bacterial community composition is poorly known. Quantitative PCR and high-throughput sequencing targeting the bacterial 16S rRNA gene were employed to characterize the bacterial community composition of long-term fertilized paddy soils treated with nitrogen (N), phosphorus (P), potassium (K), and Si (NPK + Si), with NPK or not fertilized (control). The NPK + Si fertilization significantly increased the urease and dehydrogenase activity. The relative abundance of Actinobacteria was significantly higher in the NPK + Si soil than in other two soils. Linear discriminant analysis (LDA) and effect size (LEfSe) analysis demonstrated that Actinobacteria and its associated taxonomic groups were significantly more abundant in the NPK + Si-treated plots. The bacterial community composition of the NPK + Si soil was significantly different from those of NPK and control soils as shown by the ordination plot. According to distance-based regression analysis, variation in bacterial community composition was related to available SiO2 and P2O5 concentrations. Functional profiles predicted from 16S rRNA abundance data showed that the NPK + Si plots were more enriched by genes coding enzymes related to plant growth promotion compared to NPK and control plots.