The present invention relates to phosphopeptide isolation and enrichment, particularly to a highly selective and specific phosphopeptide enrichment method. The method mentioned in the invention is based on the strong interaction between zirconium phosphonate and phosphopeptide. Zirconium phosphonate is immobilized on the surface of matrix for phosphopeptide enrichment. Zirconium phosphonate could be immobilized on chip surface, it can also be immobilized on chromatographic matrix for isolation and purification of phosphopeptides. The method shows high specificity for phosphopeptides, it can be applied to purify and enrich low abundance phosphopeptide from biological samples.