Anthraquinones are widely distributed in higher plants and possess broad biological activities. The conventional separation procedures for isolating anthraquinones from the plant crude extracts require multiple extraction, concentration, and column chromatography steps. In this study, we synthesized three alizarin (AZ)-modified Fe3O4 nanoparticles (Fe3O4@AZ, Fe3O4@SiO2-AZ, and Fe3O4@SiO2-PEI-AZ) by thermal solubilization method. Fe3O4@SiO2-PEI-AZ showed strong magnetic responsiveness, high methanol/water dispersion, good recyclability, and high loading capacity for anthraquinones. To evaluate the feasibility of using Fe3O4@SiO2-PEI-AZ for separating various aromatic compounds, we employed molecular dynamics simulations to predict the adsorption/desorption effects of PEI-AZ for various aromatic compounds in different methanol concentrations. The results showed that the anthraquinones could be efficiently separated from the monocyclic and bicyclic aromatic compounds by adjusting the methanol/water ratio. The Fe3O4@SiO2-PEI-AZ nanoparticles were then used to separate the anthraquinones from the rhubarb extract. At 5% methanol, all the anthraquinones were adsorbed by the nanoparticles, thus allowing their separation from other components in the crude extract. Compared with the conventional separation methods, this adsorption method has the advantages of high adsorption specificity, simple operation, and solvent saving. This method sheds light on the future application of functionalized Fe3O4 magnetic nanoparticles to selectively separate desired components from complex plant and microbial crude extracts.