Reasonable application of selenium (Se) fertilizer is bene cial for improving Se contents in grains and can affect soil ecology. No study has compared Se fertilizer application methods on bioforti cation, yield, and soil bacterial community. This study investigated the effects of topsoil (T), foliar (S), and soil+foliar (TS) application of Se fertilizer on oats. TS treatment signi cantly increased oat yield compared with the control and S. The Se content in grains was increased in the order of TS > S > T. T and TS increased the nutrients, soil organic matter, activities of urease, alkaline phosphatase, and sucrose, as well as the diversity and abundance of soil bacterial communities. According to PCA analysis, TS and T increased the relative abundance of bacteria involved in the decomposition of organic matter, such as Proteobacteria, Chloro exi, and Bacteroidetes, while reduced Granulicella, Bacillus, Raoultella, Lactococcus, Klebsiella, and Pseudomonas. Furthermore, TS signi cantly increased the relative abundance of Aciditeromonas, Gemmatimonas, Geobacter, and Thiobacter. While, T signi cantly increased the abundance of Lysobacter, Holophaga, Candidatus-Koribacter, Povalibacter, and Pyrinomonas. S did not signi cantly change the bacterial communities. The redundancy analysis revealed that soil nutrients and enzyme activities were positively correlated with the abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes, Planctomycetes, and Chloro exi, but negatively correlated with the abundance of Proteobacteria and Firmicutes. Thus, a combined application of foliar and soil Se proved most conducive for achieving higher yield, grain Se content, and improving bacterial community structure and functional gene expression in rhizosphere soil.