Herbal medicines (HMs) usually consist of complex matrices of phytochemical compounds responsible for their efficacy. Supercritical fluid chromatography (SFC) and ultra-high performance SFC (UHPSFC) are efficient techniques that can be advantageously used for the analysis of complex HMs. Here, the comprehensive UHPSFC methods were established for separation of similar flavonoids, chemical profiling and differentiation, and quality assessment of Epimedium species (EPs). An efficient separation of 12 polar flavonoids was enabled in UHPSFC with an important additive, oxalic acid. Then, 51 flavonoids were characterized, and 28 potential markers enabling the differentiation of E. wushanense from other four species were discovered by UHPSFC-QTOF/MS combined pattern recognition multivariate statistical analysis. Additionally, the UHPSFC-PDA was developed and validated for simultaneous quantification of 7 predominant flavonoids in five EPs, and remarkable variation in their contents was observed. This integrated UHPSFC approach has potential applications in systematic analysis and quality evaluation of HMs containing hydrophilic flavonoids. (C) 2019 Elsevier B.V. All rights reserved.