Herbra Epimedii is a common and widely used traditional Chinese medicine for thousands of years. Epimedium alpinum L. is one of the representative herb of Epimedium species in Europe, which is used as a diaphoretic and applied in breast illness in folk medicine. In this paper, an efficient UHPLC-Q-TOF-MS method was established for rapid discovery and identification of prenylated flavonoid glucosides in E. alpinum from Croatia. Based on the MS fragment pathways, rules and intensity of 12 reference compounds in negative and positive ion mode, the kinds of substituents and site of saccharides linkage of 79 prenylated flavonoid glucosides were tentatively characterized. Different substituents at C-3 and C-4 in the ring B formed four skeletons, including skeleton A with hydrogen and hydroxyl, skeleton B with hydrogen and methoxyl, skeleton C with hydroxyl and methoxyl and skeleton D with two hydroxyls, were identified in E. alpinum. Based on our knowledge, the skeleton D was first identified in herb medicine and 23 new compounds with skeleton D were characterized. According to these findings, prenylated flavonoids glucosides of 40 leaves, rhizomes, buds and tissue cultural products of E. alpinum were further systematically investigated. Chemicals in E. alpinum from Croatia were obviously different from those in E. koreanum Nakai and E. brevicomu Maxim from China via principal component analysis (PCA). This study provide an effective strategy for new compounds discovery in herbal extract, which is helpful to quality control and pharmacological evaluation of E. alpinum from Croatia.