Although fish and shrimp are commonly consumed in daily life and recognized as nutrient-rich species, global profiling of the endogenous nutrients in these species is lacking. Here, we optimized the sample preparation and data acquisition methods of metabolomics to comprehensively characterize the nutrients in selected fish and shrimp species and compared them with those in beef, leading to the identification of 71 differentially expressed metabolites. Of these, docosahexaenoic acid, taurine, choline and (lyso)phosphatidylcholines were found to be abundant in the examined fish species, while several nonessential amino acids were rich in the analyzed shrimp samples. Subsequently, the biological functions of the metabolites rich in shrimp were queried. Intriguingly, the examined nutrients exemplified by proline can significantly mitigate the lipopolysaccharide (LPS)-stimulated inflammatory responses in BV2 cells and RAW264.7 cells. Collectively, our findings imply that the dietary intake of certain fish and shrimp species may benefit human health through alleviating inflammatory responses.