The primary objective of this study is to facilitate the conversion of inorganic selenium (Se) into organic Se within plants via assimilation, subsequently feeding it to livestock and poultry to enhance healthy animal production and yield Se-enriched livestock and poultry products. Therefore, it is imperative to first investigate the impact of varying Se doses on the agronomic traits of plants as well as their forage storage and processing. This experiment investigated the effect of Se fertilizer application on the fermentation quality, chemical composition, and bacterial community of Pennisetum americanum × Pennisetum purpureum cv Minmu 7 (HPM7). There were nine Se fertilizer dissolution levels of HPM7 treated, which were 0 mg/kg (Se0), 0.50 mg/kg (Se1), 1.00 mg/kg (Se2), 2.00 mg/kg (Se3), 5.00 mg/kg (Se4), 10.00 mg/kg (Se5), 20.00 mg/kg (Se6), 30.00 mg/kg (Se7), 40.00 mg/kg (Se8), and 50.00 mg/kg (Se9). The results showed that after silage, the water-soluble carbohydrates of Se1, Se2, and Se3 were lower than Se0, and the pH of Se3, Se4, and Se6 were lower than the Se0. The number of OTUs in the nine groups was sequentially Se1 > Se2 > Se3 > Se8 > Se6 > Se5 > Se7 > Se4 > Se0. The dominant bacterial phyla in silage samples were Firmicutes and Proteobacteria. Compared with Se0, Bacterial Shannon index in Se1 and Se2 were higher, while Chao1 and ACE indices of Se1, Se2, Se3, Se5, and Se6 were higher. A beta diversity analysis indicated that the Se1 exhibited the highest number of significant biomarkers. Escherichia coli between Se0 and Se3 and Clostridium sardiniense and Clostridium perfringens between Se0 and Se1 exhibited significant differences at a species level. The most abundant pathways for metabolism were membrane transport, carbohydrate metabolism, translation, replication, repair, and amino acid metabolism. The correlation analysis indicated that the dry matter content was negatively correlated with Bacillus (p < 0.01), Lactobacillus (p < 0.05), Pediococcus (p < 0.05), and Hirschia (p < 0.05); the contents of neutral detergent fiber and hemi-cellulose were positively correlated with Lactobacillus (p < 0.05, p < 0.01). The protein content was negatively correlated with proteus (p < 0.05). This study demonstrated that the application of Se fertilizer could enhance the Se content in HPM7. The optimal fertilization concentration was found to range from 0.50 to 2.00 mg/kg, which facilitates the metabolism of soluble carbohydrates and enhances both the fermentation quality and microbial relative abundance of HPM7 silage.
