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In the present study, we investigated the preservative effects of chitosan (CS) coatings, with and without thyme essential oil (TEO), combined with vacuum impregnation (VI) on maintaining the quality of snakehead fillets during chilled storage. The results showed that the VI treatment significantly inhibited drip loss, discoloration, microbial proliferation, and the accumulation of biogenic amines (BAs) in the sneakhead fillets. Compared to the control, the fillets treated with VI of 1% (w/w) CS and 1.5% (w/w) TEO (i.e., CSTEO) showed significant reductions in both psychrophiles and mesophiles, with a 2.66 log CFU/g decrease in total viable count (TVC) on day 3 and a 1.89 log CFU/g decline in TVC on day 9, respectively. In addition, the content of histamine and putrescine in the CSTEO groups was maintained at ∼1.14 and 3.23 mg/kg during the 12‐day chilled storage, respectively. A total of 100 chemical compounds were tentatively identified using untargeted metabolomics approaches. The multivariate analysis further revealed that the combination of VI and CSTEO maintained fish quality mainly through preventing lipid oxidation and protein degradation. Overall, the VI‐CSTEO treatment effectively maintained the fish quality during storage at 4°C, with minimum microbial proliferation and accumulation of BAs. Practical Application: The preservative effect of chitosan coatings containing thyme essential oil combined with vacuum impregnation on snakehead quality during the 12‐day chilled storage was verified, and the underlying mechanisms were deciphered through integrated metabolomics approaches. Our study could provide a promising strategy for the preservation of aquatic products. [ABSTRACT FROM AUTHOR]