The development of additional functions and applications of covalent organic framework (COF)-derived materials still remains highly desired. In our work, a novel COF-functionalized magnetic graphene biocomposite (MagG@COF-5) was first developed as an ultrasensitive hydrophilic matrix via a facile self-assembly method for efficiently recognizing N-linked glycopeptides. By integrating the characteristics of the magnetic graphene and COF-5 layer, the MagG@COF-5 owns features of an outstanding magnetic response, a high specific area, strong hydrophilic properties and a unique size-exclusion effect. Accordingly, the MagG@COF-5 biocomposite showed excellent performance in N-linked glycopeptide analysis with a low detection limit (0.5 fmol μL-1), an excellent size-exclusion effect (HRP digests/BSA, 1 : 600), good recyclability and reusability. More excitingly, the practical applicability of the biocomposite was evaluated by treatment with human serum (1 μL), in which 232 N-linked glycopeptides from 85 glycoproteins were detected. All the results demonstrate that the as-synthesized MagG@COF-5 biocomposite has huge potential for use in glycoproteome and clinical diagnosis fields. It will also open up new phases for application of COF-based materials.