Abstract: Sodium selenite was applied as a selenium fertilizer for selenium-enriched cultivation of Epimedium sagittatum (Sieb. et Zucc.) Maxim. This study investigated the effects of selenium on the absorption of Pb, Cd, Hg, and As, as well as on the accumulation of flavonoids, such as icariin, epimedin A, epimedin B, and epimedin C. Results showed that: (1) At a soil selenium concentration of 10 mg/kg, the uptake of harmful elements by E. sagittatum was inhibited, except for As, while higher selenium concentrations promoted the absorption of all harmful elements. In contrast, foliar selenium application inhibited the absorption of all four harmful elements in a dose-dependent manner. (2) Selenium enrichment in E. sagittatum showed a significant dose-dependent relationship with selenium content, and foliar selenium application promoted leaf growth. (3) Selenium enrichment dose dependently increased the accumulation of flavonoids in E. sagittatum. In conclusion, foliar selenium application may reduce the accumulation of harmful elements in E. sagittatum and improve the quality of Epimedium herbs, presenting a new approach for their development and utilization.