A novel magnetic adsorption nanomaterial was synthesized by the copolymerization of a deep eutectic solvent (DES) and chitosan (CS)-modified Fe3O4 particles. This material was proposed for the magnetic solid-phase extraction (MSPE) of flavonoids from an aqueous extract solution of herbal Epimedium folium without pretreatment. Coupled with high-performance liquid chromatography (HPLC), a rapid, environmentally friendly, and efficacious method was established and successfully applied for the enrichment, separation, and quantification of five quality marker flavonoids (viz. icariin, epimedin A, epimedin B, epimedin C, and baohuoside Ⅰ, respectively) in herbal E. folium collected from four species and 18 habitats. In addition, the physicochemical properties and morphology of Fe3O4-CS-DES were characterized by Fourier transform infrared spectroscopy, transmission electron microscopy, scanning electron microscopy, thermogravimetric analysis, X-ray diffraction, and vibrating sample magnetometry. Furthermore, key parameters, including adsorbent amount, elution solvent, and desorption factor, were optimized. Under the optimal experimental conditions, the five flavonoids were adsorbed rapidly on MSPE, which were released easily using methanol-acidified formic acid. A reversed-phase C18 column with gradient mobile phases comprising acetonitrile and formic acid water was used for analyte separation and elution. Limits of detection for the five analytes ranged from 0.5 to 2.1 ng mL−1. Coefficients of determination in analyses ranged from 0.99994 to 0.99999. Intra-day and inter-day precision ranged from 0.75 to 5.18% (n = 6) and from 2.88 to 7.52% (n = 3), respectively. Recoveries of the five analytes ranged from 80 to 110%, with relative standard deviation values of less than 10%. To the best of our knowledge, as a new adsorbent, Fe3O4-CS-DES nanoparticles were synthesized and used for the first time for the preconcentration and separation of flavonoids. This study provided a new approach for the enrichment and detection of Epimedium flavonoids in real samples.