Approximately 2.5% of the global population experience allergic reactions to seafood, making it one of the most prevalent and life-threatening allergies. Seafood allergy can lead to the disruption of the intestinal barrier, possibly due to aberrant intestinal glycosylation. In this study, the mechanisms underlying seafood allergy were explored through the lens of intestinal glycobiology. Mice were sensitized with tropomyosin, resulting in significant increases in allergy symptom scores, specific antibody and T helper 2 cytokine levels. Intestinal damage was confirmed by histopathology, as well as by assessments and levels of diamine oxidase and claudin-1. Moreover, alterations in glycosylated proteins within the jejunum were analyzed using high-throughput mass spectrometry and the pGlyco3.0 search engine. Precision N-glycoproteomics analysis yielded 2283 glycosylation peptides corresponding to 655 unique glycosylation sites on 399 proteins. Differential expression and enrichment analyses revealed that differentially expressed glycoproteins were significantly enriched in the extracellular matrix (ECM)-receptor interaction pathway and focal adhesion pathway. In conclusion, tropomyosin sensitization leads to intestinal glycome changes, accompanied by remodeling of the intestinal ECM. Our research establishes an essential theoretical basis for targeting the intestinal glycome and ECM remodeling in a precise and fine-tuned manner for the treatment of food allergies.