In this study, morin magnetic molecularly imprinted polymers (Morin‐MMIPs) were synthesized based on magnetic nanoparticles and surface molecularly imprinted technology with superparamagnetism and extraction selectivity. The polymers allowed the separating of morin from complex matrices in the presence of an external magnetic field with no need for centrifugation or filtration. The microstructure of the polymers was characterized by scanning electron microscopy and transmission electron microscopy. Meanwhile, the functional group and magnetic properties of the polymers were characterized using Fourier transform infrared spectroscopy (FT‐IR) and magnetic vibration meter (VSM). The maximum adsorption capacity of MMIPs was 3.24 mg/g, which was 2.55 times higher than that of MNIPs (1.27 mg/g). Morin was quantified by HPLC‐DAD, which showed good linearity in the concentration range of 0.05–60 µg/ml with the correlation coefficient R2 = 0.9993. The limit of detection (LOD) was 0.08 µg/ml, and the spiked recoveries were 87.5–106.8%. The calculation of the adsorption isotherm and kinetic model revealed the adsorption mechanisms, and the adsorption process was consistent with the Langmuir adsorption isotherm and pseudo‐secondary kinetic models. Likewise, the material has been successfully used to extract and separate morin from food samples. The method reported in this paper has the advantages of fast adsorption speed, high selectivity, and environmental friendliness. It provided a reliable method for the separation and detection of morin or other natural products.