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 withultravioletdetection 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.