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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 <i>Bacillus velezensis</i> through physiological and biochemical tests as well as 16S rDNA sequencing. This study found that D-2 exhibits antibacterial effects on several microorganisms, including <i>Escherichia coli</i>, <i>Staphylococcus aureus</i>, <i>Salmonella enteritidis</i>, <i>Aspergillus niger</i>, <i>Saccharomyces cerevisiae</i>, <i>Fusarium oxysporum</i>, and <i>Fusarium graminearum.</i> However, it has no adverse effect on <i>Lactobacillus reuteri</i>, <i>Enterococcus faecium</i>, or <i>Lactobacillus casei.</i> 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.