Mass　spectrometry　(MS)-based　in-depth　glycoproteomics　demands　additional　sample　pretreatment　to　remove　interference　from　nonglycoproteins　and　to　enhance　the　precise　identification　of　low-abundance　glycopeptides.　Herein,　an　attractive　strategy　was　proposed　for　preparing　core-shell-structured　phenylboronic　acid-immobilized　magnetic　covalent　organic　frameworks　(MCNCs@COF@PBA),　which　were　comprised　of　magnetite　colloid　nanocrystal　clusters　(MCNCs)　adopted　as　a　core　and　phenylboronic　acid-modified　covalent　organic　frameworks　(COFs)　served　as　the　shell　via　a　facile　azide-alkyne　＂click＂　reaction　and　the　first　application　in　the　specific　enrichment　of　N-linked　glycopeptides.　The　resultant　MCNCs@COF@PBA　composites　exhibited　high　magnetic　responsiveness,　uniform　mesoporous　structure,　and　high　surface　area,　as　well　as　abundant　binding　sites,　which　could　act　as　an　efficient　adsorbent　for　specific　capture　of　the　N-linked　glycopeptides　from　the　digested　glycoprotein　and　protein　mixture　along　with　simultaneous　protein　repelling.　These　results　confirmed　that　the　MCNCs@COF@PBA　composites　had　some　distinct　advantages　in　the　enrichment　of　the　N-linked　glycopeptides,　which　included　outstanding　selectivity　(HRP:BSA　=　1:600),　good　sensitivity　(100　amol),　high　enrichment　recovery　(∼93%　±　3%)　and　rapid　magnetic　separation　(∼1　min).　Furthermore,　the　developed　MCNCs@COF@PBA-based　MS　method　could　be　successfully　applied　to　analyze　glycopeptides　in　exosomes　secreted　from　HeLa　cell.　This　study　not　only　provides　a　potential　selective　enrichment　platform　for　comprehensive　N-glycoproteome　profiling,　but　also　opens　up　a　new　avenue　for　universal　functionalization　of　COFs-based　materials.　©　2019　American　Chemical　Society.