Large scale characterization of phosphoproteins requires highly specific methods for purification of phosphopeptides because of the low abundance of phosphoproteins and substoichiometry of phosphorylation. Enrichment of phosphopeptides from complex peptide mixtures by immobilized metal affinity chromatography (IMAC) is a popular way to perform phosphoproteome analysis. However, conventional IMAC adsorbents with iminodiacetic acid as chelating group to immobilize Fe3+ lack enough specificity for efficient phosphoproteome analysis. Here we reported a novel IMAC adsorbent through Zr4+ chelating to the phosphophate modified poly(glycidyl methacrylate–co-ethylene dimethacrylate) polymer beads. The high specificity of Zr4+-IMAC adsorbent was demonstrated by effectively enriching phosphopeptides from the digest mixture of phosphoprotein (a or ß-casein) and bovine serum albumin with molar ratio at 1:100. Zr4+-IMAC adsorbent was also successfully applied for the analysis of mouse liver phosphoproteome which resulted in the identification of 153 phosphopeptides (163 phosphorylation sites) from 133 proteins in mouse liver lysate. Significantly more phosphopeptides were identified than that of conventional Fe3+-IMAC approach, which indicated the excellent performance of Zr4+-IMAC approach. The high specificity of Zr4+-IMAC adsorbent was found to be mainly resulted from the strong interaction between chelating Zr4+ and phosphate group on phosphopeptides. Enrichment of phosphopeptides by Zr4+-IMAC provides a powerful approach for large scale phosphoproteome analysis.