Protein phosphorylation is one of the most important post-translational modifications.It is an active research area to study phosphoproteomics for discovery of disease biomarkers and druggable targets.Here we report the development of superparamagnetic Fe3O4@mZrO2 core-shell microspheres with mesoporous structures for highly efficient enrichment of phosphopeptides.We have demonstrated that the mesoporous ZrO2 layer dramatically improves the selective enrichment of phosphopeptides.Our approach allows for in-situ elution and sensitive identification of both mono-phosphorylated and multi-phosphorylated peptides in MALDI-TOF mass spectrometry,with the detection limit of down to the femtomole range.The target phosphopeptides can reliably be enriched for MS analysis from various complex samples including the spiked protein digests and tumor cell lysates.The Fe3O4@mZrO2 core-shell microspheres promise a useful tool for phosphoproteomics by allowing for highly efficient and selective enrichment of the crucial signaling regulators in a low abundance.