Epimedium has beneficial effects in nourishing and building up the body and is widely used in practical production of Epimedium preparations. As one of the major active compounds in Epimedium preparations, icariin is be used as a quality control index of industrial manufacture. However, content of icariin was observed to increase to uncertain extent in pharmaceutical production, which might bring difficulties in quality control. The content fluctuation mainly occurred in high-temperature extraction process. The aim of this study is to investigate what happen to flavonol-glycosides in Epimedium under heating treatment. Ultra-Performance Liquid Chromatography-Linear Ion Trap Mass Spectrometer was applied to profile the transformation rule of flavonol-glycosides in Epimedium and search for an explanation for the increase in icariin content under heating treatment. 56 compounds were found to have significantly changed and their structures were identified, among which 15 flavonol-glycosides were proposed to play a role in icariin content variation. Further studies were conducted based on 8 flavonol-glycosides standard substances to obtain more credible data. Finally, Baohuoside II, 2"-o-rhamnosylicariside II, Epimedin A1, Epimedin A, Epimedin B, Epimedin C, Baohuoside I and Anhydroicaritin were found to transform into icariin during the heating process. This study provides an evidence for the quality control study of Epimedium preparation, as well as reference for chemical researches in natural pharmacy.