Chemical　modification　of　covalent　organic　frameworks　(COFs)　is　indispensable　for　integrating　functionalities　of　greater　complexity　and　accessing　advanced　COF　materials　suitable　for　more　potential　applications.　Reported　here　is　a　novel　strategy　for　fabricating　controllable　core　shell　structured　Zr4+-immobilized　magnetic　COFs　(MCNC@COF@Zr4+)　composed　of　a　high-magnetic-response　magnetic　colloid　nanocrystal　cluster　(MCNC)　core,　Zr4+　ion-functionalized　two-dimensional　COFs　as　the　shell　by　sequential　postsynthetic　functionalization　and,　for　the　first　time,　the　application　of　the　MCNC@COF@Zr4+　composites　for　efficient　and　selective　enrichment　of　phosphopeptides.　The　as-prepared　MCNC@COF@Zr4+　composites　possess　regular　porosity　with　large　surface　areas,　high　Zr4+　loading　amount,　strong　magnetic　responsiveness,　and　good　thermal/chemical　stability,　which　can　serve　as　an　ideal　adsorbent　for　selective　enrichment　of　phosphopeptides　and　simultaneous　size　exclusion　of　biomacromolecules,　such　as　proteins.　The　high　detection　sensitivity　(10　fmol)　together　with　the　excellent　recovery　of　phosphopeptides　is　also　obtained.　These　outstanding　features　suggest　that　the　MCNC@COF@Zr4+　composites　are　of　great　benefit　for　pretreatment　prior　to　mass　spectrometry　analysis　of　phosphopeptides.　In　addition,　the　performance　of　the　developed　approach　in　selective　enrichment　of　phosphopeptides　from　the　tryptic　digests　of　defatted　milk　and　directly　specific　capture　of　endogenous　phosphopeptides　from　human　serum　gives　powerful　proof　for　its　high　selectivity　and　effectiveness　in　identifying　the　low-abundance　phosphopeptides　from　complicated　biological　samples.　This　study　not　only　provides　a　strategy　for　versatile　functionalization　of　magnetic　COFs　but　also　opens　a　new　avenue　in　their　use　in　phosphoproteome　analysis.