As one of the most prevalent and crucial post-translational modifications, glycosylation plays a role in diverse biological processes and its abnormal expression is closely associated with various diseases. The direct mass spectrometry analysis of glycoproteins is still a challenge due to their low abundance and the strong ion inhibitory effect from unmodified proteins. In this study, we developed a magnetic cyanidin material, and facilely realized efficient glycoprotein enrichment based on synergistic hydrophilic-electrostatic interactions. The developed method was applied to glycopeptide detection in real human saliva samples and obvious characteristic glycopeptide peaks were detected after enrichment. In addition, glycopeptides were successfully identified in HepG2 cells, demonstrating that the synthesized material broadens the possibility of discovering biomarkers toward hepatocellular carcinoma.