Despite the strong antihepatotoxic, antioxidant, and antitumor properties of lignans from Schisandra chinensis, their applications in new drug development, bioscience and functional foods, etc. are limited because of their low abundance and complex coextractions. In this study, a magnetic separation method has been developed based on polyethylenimine-modified magnetic nanoparticles to rapidly and effectively separate and purify the lignans from S. chinensis crude extracts through cation-π interaction and electrostatic adsorption. The magnetic nanoparticles were characterized by transmission electron microscopy, vibrating sample magnetometry, Fourier transform infrared spectroscopy, and X-ray diffraction. Polyethylenimine-modified magnetic nanoparticles showed a spherical-shaped morphology and the average size was about 10 nm with superparamagnetism. Under the pH 7.4, polyethylenimine modified magnetic nanoparticles can remove a lot of coextracts. The range of detection limits and quantification limits was 0.27-0.34 and 0.89-1.13 ng/mL, respectively. Compared with other common methods, the magnetic separation method proposed in this study is much simpler and more effective through both strong cation-π interaction and electrostatic interaction.