Chilled duck meat is a popularly consumed meat in China but easily perishes at room/low temperature. Kojic acid is usually used as an antimicrobial. This study investigated the sensory scores, total bacteria number, and total volatile base nitrogen (TVB-N) value of chilled duck meat under kojic acid treatment during storage. The results presented that kojic acid suppressed the growth of spoilage bacteria and prolonged the shelf-life of chilled duck meat by at least two days. In further investigation, the bacterial community composition was explored through high-throughput sequencing. Pseudomonas spp. were the predominant spoilage bacteria after 6-day storage and were significantly suppressed by kojic acid. Besides, Brochothrix showed drug resistance and became the dominant bacteria in the kojic acid treated sample after 6-day storage. In conclusion, kojic acid maintained the sensorial, chemical, and microbial quality of duck meat stored at low temperatures. Meanwhile, kojic acid enriched the bacteria composition and showed strong antimicrobial activity against Pseudomonas spp.