Magnetic polymer microbeads and a method for preparing the same are provided. The method for preparing the magnetic polymer microbeads includes the following steps: preparing polymer particles; immersing the polymer particles into a solution in order to swell the polymer particles; adding magnetic nanoparticles to the solution and allowing the magnetic nanoparticles to enter an interior of the polymer particles; and separating the polymer particles from the solution, wherein the polymer particle is made of polystyrene, or a copolymer containing styrene, and the solution includes a medium polar solvent. The average particle size of the magnetic polymer microbeads of the present invention ranges from submicrons to microns. The magnetic polymer microbeads of the present invention have high magnetization, and the various functional groups can be introduced onto the surfaces thereof. Therefore, the magnetic polymer microbeads of the present invention can be applied in many areas, and thereby they have high economic value.