The accurate characterization of low abundance phosphopeptides based on mass spectrometry (MS) techniques remains a challenge due to signal suppression by the large excess of interfering proteins and non-phosphopeptides. This demands better methods to effectively enrich phosphopeptides prior to MS analysis. In the current work, facilely synthesized Zr-based metal-organic frameworks (MOFs) of UiO-66 and UiO-67 have been successfully exploited as novel affinity materials for the enrichment and analysis of phosphopeptides. Thanks to their abundantly existent and naturally exposed Zr-O clusters, intrinsically large surface areas and highly ordered open cavities, UiO-66 and UiO-67 exhibited sensitive and specific enrichment of phosphopeptides with an interesting molecular sieving effect. An optimized protocol for loading, washing and elution was developed. Under these most optimized conditions, specific accumulation was demonstrated by the selective enrichment of phosphopeptides in the presence of abundant non-phosphorylated species. Meanwhile, high-abundance interfering proteins could be effectively excluded during the enrichment process. Additionally, the MOFs have also been successfully used to enrich phosphopeptides from human serum. These merits combined with their high chemical and thermal stabilities, make UiO-66 and UiO-67 highly promising for applications in phosphopeptidome research.