Protein glycosylations play important roles in various biological processes and in the disease progression of organisms. The development of specific enrichment materials and strategies before mass spectrometric analysis was a prerequisite to glycoproteomic analysis due to the difficulty caused by substoichiometric levels of glycoproteins. In this work, novel magnetic covalent organic frameworks (denoted as Fe3O4@TpPa-1) were first developed using only a two-step solvothermal reaction and then applied in the hydrophilic enrichment of glycopeptides. Sea urchin-type composites with super-paramagnetic properties were constructed by in situ growth of TpPa-1 covalent organic frameworks on the surface of magnetic nanoparticles. A total of 37 and 22 glycopeptides could be easily detected from IgG and HRP digests, respectively, by hydrophilic enrichment with the newly developed materials. An ultralow detection limit (28 fmol), satisfactory selectivity and high recovery could be achieved using Fe3O4@TpPa-1. The material's excellent enrichment performance was also demonstrated using glycopeptide analysis in real complex samples. Within three independent replicates, 228 glycopeptides corresponding to 114 glycoproteins could be detected from human serum digests, which is better than the performance obtained by commercial HILIC materials. The results suggest that covalent organic frameworks show potential for application in glycoproteomic studies.