In order to analyze the mechanism of the quality change of grass carp meat during cold storage, grass carp meat was stored at 4 ℃ and evaluated for changes in the composition of small-molecular-mass metabolites and ultrastructure after 24 and 72 h by gas chromatography time of flight-mass spectrometry (GC-TOF-MS) and transmission electron microscopy (TEM), respectively. As refrigeration time increased, the gap between muscle fibers became larger, the arrangement became disordered, and some sarcomeres were broken. A total of 211 metabolites were identified by metabolomics, of which 42 metabolites changed by more than 1.5 times (P < 0.05). The accumulation of lactic acid and phosphoric acid was the major reason for the pH decrease of fish meat. It was found that succinic acid was the only tricarboxylic acid (TCA) cycle metabolite that was significantly reduced (P < 0.05), which was converted into 4-hydroxybutanoic acid methyl ester and γ-aminobutyric acid, and levels of these three metabolites may be potential indicators of of the freshness of refrigerated grass carp meat. The contents of polyunsaturated fatty acids (such as linolenic acid and arachidonic acid) decreased significantly (P < 0.05), while the content of azelaic acid increased significantly (P < 0.05). Moreover, the contents of valine and L-cysteine increased significantly during cold storage (P < 0.05), and lipid oxidation preceded protein degradation. Plant secondary metabolites (piperine, naringenin, methyl jasmonate, loganin, α-ascarisin, abietic acid, and 3,4-dihydroxymandelic acid) contained in grass carp meat could affect the nucleotide metabolism and taste of fish meat by inhibiting xanthine oxidase.