In this study, modified magnetic chitosan microparticles (MCDs) were fabricated and used as adsorbents for the removal of Food Yellow 3 (FY3) and Acid Yellow 23 (AY23) from aqueous solution. The magnetic microparticles were characterized by scanning electronic microscope, Brunauer-Emmett-Teller specific surface area, elemental analysis, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, thermogravimetry analysis, differential scanning calorimetry, and vibrating-sample magnetometer. Then, the effects of pH value, initial dye concentration, and contact time on the adsorption of FY3 and AY23 by MCDs were investigated. Evidently, MCDs showed excellent adsorption performance for both food dyes, and their adsorption capacities (833.33 mg/g for FY3 and 666.67 mg/g for AY23) were considerably higher than those of unmodified adsorbents, which could be attributed to the electrostatic interaction and ion exchange between the grafted cationic polymer and food dyes. Adsorption isotherm and kinetic data of the magnetic microparticles were well fitted by Langmuir isotherm and pseudo-second-order kinetic model, respectively. The regeneration and reusability of MCDs were also explored. Results showed that more than 80% adsorption capacities of MCDs for FY3 and AY23 remained after five adsorption-desorption cycles.