A novel affinity peptide S1 (LIDHEWKENYFPLSF) was screened out via a "one bead one compound" (OBOC) approach on a microarray device. It was identified that S1 could specifically recognize and bind to vascular endothelial growth factor receptor 2 (VEGFR2), which is an angiogenesis biomarker. Moreover, S1-functionalized liposomes (S1-LS) could achieve efficient nanoscale drug delivery under the conditions of VEGFR2-overexpression in vitro and in vivo. It was demonstrated that S1-LS would be a promising VEGFR2-targeting drug delivery system.