Epimedii Folium (EF) is a commonly used traditional Chinese drug that includes many species. In Chinese Pharmacopoeia (2020 edition), EF includes Epimedium brevicornu Maxim, E. Sagittatum (Sieb. et Zucc) Maxim, E. pubescens Maxim, E. koreanum Nakai, and Epimedium Wushanense T.S. Ying. It has been reported that the active constituents in EF are different, resulting in the uneven quality of commercial medicinal materials. To explore the specific differences and make a comprehensive quality evaluation of EF, we established an analytical method to simultaneously detect 45 constituents including 23 flavonoids, 4 phenolic acids, 12 amino acids, 5 nucleosides, and 1 alkaloid in 5 species of EF, based on ultrafast performance liquid chromatography coupled with triple quadrupole-linear ion trap mass spectrometry (UFLC-QTRAP-MS/MS). In addition, orthogonal partial least squares discriminant analysis (OPLS-DA), analysis of variance (ANOVA), and grey correlation analysis (GRA) were used to discriminate and evaluate different species of samples. The results showed that EF could be divided into three categories and EBM was superior to the other four species. This study provides data basis for the comprehensive evaluation and a new perspective on the quality control of EF from different species.