A porous hydrophilic affinity bead consisting of graphene oxide and chitosan (pGC) with the honeycomb-biomimetic microchannels has beensynthesized and applied as hydrophilic adsorbent for selective capture of glycopeptides. The pGC beads have open-porous structure, honeycomb-like microchannels, large interior voids, and hydrophilic property. Based on the multivalent hydrophilic interactions between glycan moieties on glycopeptides and amino groups and hydroxyl groups on chitosan, the glycopeptides were enriched and separated by pGC beads. The pGC beads exhibit high sensitivity (detection limit, 5fmol), binding capacity (111.1mg/g), enrichment selectivity (molar ratio of human IgG to BSA tryptic digests of 1:200), and recovery yield (89.78%). By combing pGC beads and nano LC-MS/MS analysis, a total of 325 N-glycosylated peptides corresponding to 152 N-glycosylated proteins were identified from 2μL human serum. These experimental results demonstrate the practical application of the method in glycoproteomics research. Graphical abstract Schematic representation of fabrication for porous hydrophilic affinity beads (pGC) with honeycomb-biomimetic microchannels based on graphene oxide (GO) and chitosan (CS). The pGC was successfully applied to capturing and identifying low-abundant glycopeptides from biological samples.