A composite emulsion was created by incorporating 4% (m/m) soybean protein isolate and 25% (m/m) soybean oil into a mixture containing 0.5% (m/m) chitosan and 1% (m/m) thymol. By comparing changes in total volatile basic nitrogen content, aerobic bacteria count, pH, biogenic amines content, volatile components, and microbial species in fish meat after storage at different times, the study explored the impact of composite emulsions on the quality of largemouth bass fillets during storage. Our results show that this composite emulsion effectively delayed the increase in total volatile basic nitrogen content, aerobic bacterial count, putrescine, cadaverine, and histamine contents of largemouth bass fillets during storage at 10 °C, extending the shelf life to 16 days. The primary spoilage compounds observed during the storage of largemouth bass fillets were isopentyl butyrate-M, 3-methylpentanoic acid, 4-methyl-2-pentanone, 4-methylthiazole, ethyl 2-methylbutyrate, and 2-butanol-D. Furthermore, the addition of the emulsion during storage effectively reduced the relative abundance of Aeromonas and Citrobacter, while also decreasing the generation of isoamyl butyrate-M and 2-methylbutyraldehyde-M. In conclusion, the combination of chitosan and thymol coating not only delayed the deterioration of largemouth bass fillet quality during storage but also inhibited the growth of spoilage bacteria and reduced the production of volatile spoilage compounds. Therefore, this study can provide valuable reference for the preservation of largemouth bass and the application of low temperature logistics and transportation for aquatic products.