Molecularly imprinted polymeric microbeads (MIPMs) were prepared by using a magnetic impeller by the modified suspension polymerization method with D-phenylalanine (Phe) as the water-soluble template without derivatization, methacrylic acid as the functional monomer, ethylene glycol dimethacrylate as the cross-linker, toluene as the porogen, polyvinyl alcohol as the stabilizer, and sodium dodecyl sulfate as the surfactant. The mean diameter of MIPMs decreased from 12.45 µm to 8.86 µm by using a simple magnetic impeller instead of a conventional simple straight-blade turbine impeller during suspension polymerization. The adsorption selectivity of MIPMs prepared with a magnetic impeller was much improved as compared to the adsorption selectivity of MIPMs prepared with a conventional simple straight-blade turbine impeller. The adsorption selectivity of MIPMs changed from reversed adsorption (less than 1) to positive (higher than 1) as the washing time increased after suspension polymerization.