Icariin (ICA), a major flavonoid responsible for the pharmacological actions of Herba Epimedii, was found to be increased significantly after the heating process. The increase of ICA was considered to be due to the transformation of other flavonoids, in particular, epimedin (EPI) A–C. This novel study demonstrated that the increase of ICA in Epimedium. koreanum was induced mainly through the conversion of 3′′′-carbonyl-2′′-β-l-quinovosyl icariin (CQICA) by deglycosylation during the heating process. Furthermore, the comparative analysis of the changes of CQICA and ICA in four raw Epimedium species (EPs) designated in the Chinese Pharmacopoeia revealed that the increase of ICA during the heating process was associated with the presence of CQICA in EPs. The present study provided scientific evidence for the conversion of CQICA into ICA, correcting the understanding of the transformation of EPI A−C into ICA. The results provided a reasonable scientific basis for the traditional use of processed Herba Epimedii, and might be helpful for the quality assessment of EPs.