Prenyl flavonoid glycosides and phenolic acids are constituents of the medicinal plant Epimedium koreanum Nakai (EK). An efficient method was developed to enrich these compounds and identify them, using ultra performance liquid chromatography combined with Q-TOF-MS, and a "click oligo (ethylene glycol)" (Click OEG) column. Using this method, 51 prenyl flavonoid glycosides and 18 phenolic acids were identified or tentatively identified. Of these, 11 prenyl flavonoid glycosides and 4 phenolic acids were new compounds, and 7 phenolic acids were newly identified in EK. Therefore, MS combined with selective enrichment provided a powerful means for analyzing prenyl flavonoid glycosides and phenolic acids.