Abstract: In this work, a molecular docking method and solvation model in computer simulation were applied to screen dummy template and bi-functional monomer simultaneously in the rational design of a magnetic molecularly imprinted polymer. According to the results of computer simulation, quercetin as dummy template while methacrylic acid and 4-vinylpyridine as bi-functional monomer could form hydrogen bonds and π-π interaction in pre-assembly system which contributes for the formation of highly selective molecular recognition sites and reduces the influence of the solvent to the system. Bi-functional monomer magnetic molecularly imprinted polymer as well as mono-functional monomer polymers have been prepared and systematic evaluation through scanning electron microscope, infrared spectroscopy and vibrating sample magnetometer as well as adsorption kinetics, adsorption isotherms and adsorption selectivity experiment. All results strongly supported that quercetin was suitable to set as dummy template and the bi-functional monomer polymer showed a good selectivity and affinity to target molecule zearalenone which can be applied in the extraction and purification of real samples. This work provided a good sample and a new idea of a complete set of solution in the rational design, preparation and adsorption study of a magnetic molecularly imprinted polymer using dummy template and bi-functional monomer