Abstract: Peptides derived from aquatic resources have attracted widespread attention due to their diverse biological activities and functional properties; however, they are prone to degradation, inactivation or reduced bioavailability during processing, storage and gastrointestinal digestion, thereby limiting their application in food products. Glycopeptides are compounds formed by the covalent linkage of a peptide chain to a sugar chain; they possess the structural characteristics of both peptide segments and sugar chains, and demonstrate unique advantages in terms of improved stability, modulated physicochemical properties and enhanced biological activity. In recent years, glycopeptides derived from aquatic sources have attracted widespread attention due to their potential functions in cryoprotection, texture modification and flavour enhancement. This paper provides a systematic review of research progress on glycopeptides of aquatic origin, covering their main sources, preparation methods, separation and purification techniques, and structural characterisation methods. It analyses the influence of structural factors—such as monosaccharide composition, glycopeptide bond types and amino acid composition—on their activity, and summarises their application potential in food processing. The main conclusion is that, compared with non-glycosylated peptides, glycopeptides exhibit superior functional properties; glycopeptides with functional properties can be prepared through methods such as enzymatic hydrolysis and glycosylation reactions, and purification techniques can significantly enhance the purity of glycopeptides. Finally, mass spectrometry-based omics analysis platforms and bioinformatics tools can be used to precisely elucidate the structure and properties of glycopeptides. This provides a theoretical basis for their application in functional foods and the development of natural bioactive compounds.