Peptide　enrichment　before　mass　spectrometry　analysis　is　essential　for　large-scale　peptidomic　studies,　but　challenges　still　remain.　Herein,　magnetic　mesoporous　silica　microspheres　with　phenyl　group　modified　interior　pore　walls　were　prepared　by　a　facile　sol-gel　coating　strategy,　and　were　successfully　applied　for　selective　enrichment　of　phenyl-containing　peptides　in　complex　biological　samples.　The　newly　prepared　nanomaterials　possessed　abundant　silanol　groups　in　the　exterior　surface　and　numerous　phenyl　groups　in　the　interior　pore　walls,　as　well　as　a　large　surface　area　(592.6　m2/g),　large　pore　volume　(0.33　cm3/g),　uniform　mesopores　(3.8　nm),　strong　magnetic　response　(29.3　emu/g),　and　good　dispersibility　in　aqueous　solution.　As　a　result　of　the　unique　structural　properties　and　size-exclusion　effect,　the　core-shell　phenyl-functionalized　magnetic　mesoporous　silica　microspheres　exhibited　excellent　performance　in　fast　separation　and　selective　enrichment　of　phenyl-containing　peptides,　and　the　adsorption　capacity　for　bradykinin　reached　22.55　mg/g.　In　addition,　selective　enrichment　of　phenyl-containing　peptides　from　complex　samples　that　are　consist　of　peptides,　large　proteins,　and　human　serum　were　achieved　by　using　the　as-prepared　microspheres,　followed　by　high-performance　liquid　chromatography　with　ultraviolet　detection　and　electrospray　ionization　quadrupole　time-of-flight　mass　spectrometry　analysis.　These　results　demonstrated　the　as-prepared　microspheres　would　be　a　potential　candidate　for　endogenous　phenyl-containing　peptides　enrichment　and　biomarkers　discovery　in　peptidome　analysis.　©　2015　Wiley-VCH　Verlag　GmbH　&　Co.　KGaA,　Weinheim.