In this study, a novel method based on genistein magnetic molecularly imprinted polymers (Gen-MMIPs) was developed by surface molecular imprinting technique, in which genistein was used as the template molecule and Fe3O4 was used as the carrier. The synthesis of Gen-MMIPs were characterized by using of scanning electron microscopy (SEM) and transmission electron microscopy (TEM), which indicated the diameters of Gen-MMIPs were about 500 nm. Through the technique of vibrating sample magnetometer (VSM), the saturation magnetization of Gen-MMIPs were detected as 24.79 emu/g. Fourier transform infrared (FR-IR) spectroscopy showed that polymer groups were on the surface of the magnetic carrier. Adsorption experiment suggested the adsorption capability of Gen-MMIPs to genistein were 1.55 mg/g, and 2 the adsorption equilibrium was achieved within 20 min. Gen-MMIPs as dispersive solid-phase extraction adsorbent combined with HPLC was used to selectively separate genistein in soy sauce samples, the recoveries were ranged from 85.7% to 88.5% with the relative standard deviations (RSD) less than 5%, which proved this method can be used for the detection of genistein residues in real samples.