In this work, we present a facile approach for the synthesis of zirconium phosphate (ZrP)-functionalized magnetic silica mesoporous microspheres for the selective enrichment of phosphopeptides. At first, magnetic mesoporous silica microspheres were prepared by directly coating mesoporous silica onto Fe₃O₄ magnetic microspheres, and then addition of phosphate onto the magnetic mesoporous silica microspheres was performed using 3-(trihydroxysilyl)propyl methylphosphate. The obtained phosphate-modified magnetic mesoporous microspheres were monodispersed with a mean diameter of 350 nm, and had an obvious mesoporous silica shell (∼65 nm). Finally, the resultant phosphate-functionalized magnetic mesoporous microspheres were incubated in ZrOCl₂ solution with gentle stirring overnight for the loading of Zr⁴⁺ cations. The obtained Zr⁴⁺-functionalized materials were applied to the selective enrichment of phosphopeptides from both standard protein digestion and real samples. The enriched peptides were analyzed by MALDI–TOF MS and LC–ESI MS. Experimental results demonstrated that zirconium phosphonate-modified magnetic mesoporous silica microspheres show excellent potential for the selective enrichment of phosphopeptides.