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Due to high-density farming methods and poor farming environments, freshwater fish often have poor muscle texture and a fishy odor before marketing, which impacts consumer acceptance. Short-term low-salinity seawater treatment of freshwater fish before marketing has been found to improve the quality of the fish, but the mechanisms underlying this phenomenon have not yet been revealed. In this study, metabolomics technique was used based on gas chromatography-mass spectrometry (GC–MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) to screen different metabolites and predict potential metabolic pathways after treatment with low-salinity seawater. The results showed that 3838 metabolites were presented in all of the carp samples, while 62 and 64 differential metabolites were found in the comparative groups (FW, SW, and CK represented freshwater, seawater and non-transient group, respectively). Additionally, 25 and 26 metabolic pathways were enriched from these groups. Glutaric acid, PC, and creatinine might be potential biomarkers. Seawater aquaculture significantly altered the lipid metabolism, nucleotide metabolism, and amino acid metabolism of carp, enhancing its freshness and having a significant impact on its quality. This study provided insights into the metabolic changes in carp under different rearing conditions and also served as a theoretical basis for salinity treatment before freshwater fish are brought to the market. [ABSTRACT FROM AUTHOR]