Selenium (Se) is an essential trace element in living systems. In this study, we applied a spray of 50 mg/kg sodium selenite to alfalfa (Medicago sativa L.) at different stages of development (bud, initial bloom, and full bloom stages). After 0, 1, 3, 7, and 45 days of ensiling, we assessed the fermentation quality, chemical composition, and bacterial community of the alfalfa. Our findings indicated that the addition of Se led to an increase in the Se content and a decrease in the pH, acid detergent fiber (ADF), and neutral detergent fiber (NDF) contents. As ensiling fermentation progressed, the Se treatments increased the relative abundance of Lactobacillus, which was significantly greater than that in the control group (42.44% vs. 3.76%). In conclusion, the addition of sodium selenate to silage additive ensures the quality of the silage and reduces bacterial community diversity. This study provides valuable insights for the investigation of Se enrichment in alfalfa haylage silage.