The effects of air-packed (AP) and vacuum-packed (VP) on quality and microbial characteristics of silver carp (Hypophthalmichthys molitrix) fillets during chilled storage (4 ± 1 °C) were investigated. The fillets were analyzed for sensory scores, total volatile basic nitrogen (TVB-N), ATP-related compounds (ATP, IMP, HxR, and Hx), K value, and biogenic amines (BAs). The results proved that VP inhibited the increase of microorganisms, TVB-N, Hx, and putrescine in silver carp, and slowed the reduction in sensory score. Therefore, VP can be applied for preservation of the silver carp fillets to improve its quality. For identification, 16S rRNA genes of the isolated pure strains were sequenced and analyzed. On the initial day of storage, Chryseobacterium was the dominant bacterial genus. At the end of shelf life, Pseudomonas was the most common group in AP fillets and Aeromonas followed by Yersinia were found mainly in VP samples. Practical applications Silver carp (Hypophthalmichthys molitrix) are distributed widely in fresh water systems. The world aquaculture production of silver carp was 4,354,638 tons, and it ranked second highest among freshwater fish species in 2015, but they are perishable during storage because of microbial spoilage and biochemical reactions. Vacuum packaging (VP) has proved to be effective for extending the shelf-life of aquatic products by excluding oxygen that prevents the growth of spoilage bacterial. However, little information is available on the microbial succession of VP silver carp. Therefore, this work was to determine the differences of microbiological succession on chilled silver carp fillets under air-packed (AP) and VP conditions using a combination of culture-based and 16S rRNA gene analysis methods. Furthermore, this study will give valuable information about development and spoilage of VP silver carp fillets.