In this work, we demonstrate for the first time, a method to synthesize phenylboronic acid-Fe304@polydopamine (Fe3O4@ PDA-PBA) magnetic microspheres via the combination of mussel-inspired polydopamine coating and click chemistry. Uniform-size and core-shell structured Fe3O4@PDA-PBA magnetic microspheres with a core diameter of -240 nm and a shell thickness of -13 nm were obtained as identified by the characterization of the morphology, structure and composition of the synthesized microspheres. We evaluated the selectivity and binding capacity of the Fe3O4@PDA-PBA magnetic microsphcres by using standard glycoproteins (ovalbumin, immunoglobulin G and catalase) and nonglycoproteins (human serum albumin, bovine hemoglobin, myoglobin, lysozyme, and ribonuclease A) as model proteins. Adsorption experiments, SDS-PAGE and mass spectrometry analysis demonstrated that the Fe3O4@PDA-PBA magnetic microspheres had much high binding capacity and selectivity for glycoproteins/glycopeptides compared to nonglycoproteins/nonglycopeptides. In addition, the practicability of the Fe3O4@PDA-PBA magnetic microspheres was further assessed by selective capture of glycoproteins from healthy hu- man serum. The good results demonstrated its potential in glycoproteome analysis.