Once a silo has been opened, the silage inside will face challenges such as aerobic deterioration, rot, and contamination. Biocontrol bacteria, as a kind of biological antiseptic, are highly effective and natural and are gaining increasing attention. This study aimed to screen a strain with anti-microbial activity against silage spoilage microorganisms and examine its effects on the fermentation quality, aerobic stability, in vitro digestion, and methane production of silage. Lactic acid bacteria, pathogenic and rot-causing microorganisms, were used as indicators to screen the strains for putrefactive silage. The bacteriostatic spectrum, growth performance, and tolerance to the silage environment of the strain were tested. A strain named D-2 was screened from rotten whole-plant corn silage and identified as Bacillus velezensis through physiological and biochemical tests as well as 16S rDNA sequencing. This study found that D-2 exhibits antibacterial effects on several microorganisms, including Escherichia coli, Staphylococcus aureus, Salmonella enteritidis, Aspergillus niger, Saccharomyces cerevisiae, Fusarium oxysporum, and Fusarium graminearum. However, it has no adverse effect on Lactobacillus reuteri, Enterococcus faecium, or Lactobacillus casei. D-2 can attain a stable stage within 10 h and withstand temperatures of up to 70 °C. Moreover, this study found that D-2 had a high survival rate of over 97% after 48 h in a lactic acid environment with pH 4. Freshly chopped whole-plant corn was inoculated without or with D-2 and ensiled for 60 days. The results show that D-2 inoculations increase the content of water-soluble carbohydrates, acetic acid, and propionic acid in the silage and decrease the number of yeasts and molds, the NH₄⁺-N/TN ratio, and the pH. We also found that fermenting whole-plant corn with D-2 significantly increased the in vitro digestibility and the propionic acid content, while also significantly inhibiting methane production. After being exposed to air for 10 days, D-2 can still effectively reduce the total number of yeasts and molds, prevent the decrease in lactic acid bacteria, and inhibit the increase in the pH and NH₄⁺-N/TN ratio of silage products. Overall, D-2 is resistant to pathogenic and rot-causing microorganisms, allowing for easy adaptation to silage production conditions. D-2 can effectively improve aerobic stability and reduce losses in the nutritional value of silage, indicating possible applications for the prevention of silage rot and methane production.