Biocompatible and biodegradable magnetic chitosan microcapsules were successfully prepared using carboxyl-functionalized polystyrene (PS) particles as core template. First, the monodisperse PS template with an average diameter of 340 nm was made by emulsifier free emulsion polymerization. Second, the chitosan (CS) adsorbed onto the surface of the PS template and cross linked by glutaraldehyde. After removal of the PS core, CS microcapsules could be obtained. The shell thickness of CS could be controlled between 20 and 45 nm by varying the adsorption temperature. Third, the CS microcapsules were used as a microreactor, and iron oxide nanoparticles were incorporated within CS microcapsules. The structure and morphology of the PS template, core-shell PS/CS particles, and magnetic CS microcapsules were characterized by Fourier transform infrared spectroscopy and transmission electron microscopy. The adsorption of Cu2+ and Cr3+ was investigated including the effects of adsorption time, pH value, temperature, and initial concentration by the batch method. The optimal condition for adsorption of Cu2+ and Cr3+ was 30 degrees C, with a pH value of 7.0, where the saturated adsorption capacity was 104 mg/g and 159 mg/g, respectively. The adsorption isotherms obeyed the Langmuir equation, and kinetics followed a pseudo-second-order model.