Moderately marinated fish meat forms a garlic clove-like structure after cooking. However, this structure's formation mechanism and influencing factors are unclear. Therefore, this study explored the changes in protein components and potential protein markers during the formation of garlic clove-like structure. Results showed that the contents of free hydroxyproline, lysylpyridinoline, and hydroxylysylpyridinoline first increased and then decreased, the contents of decorin and elastin decreased, and TCA-soluble peptides increased slightly during the formation process of garlic clove-like structure. The Z-disk, M-line, and H bands in the myofibrils disappeared, and the myofibrils were interconnected. This was attributed to the effect of endogenous proteases (MMP, calpain, etc.) on myofibrils, collagen fibers, and proteoglycans. Proteomics data showed that the abundance of type I collagen chains, myosin, actin, and telethonin increased while proteoglycans decreased. Among them, telethonin on the Z-disk can be used as a potential protein biomarker for the formation of garlic clove-like structure.