Here we report the synthesis and characterization of magnetic Fe₃O₄ loaded chitosan microparticles for low cost, biocompatible heavy metal removal. Magnetic Fe₃O₄ loaded chitosan microparticles are prepared based on ionic gelation and characterized by Transmission electron microscope (TEM), Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction (XRD) respectively, which confirm that magnetic Fe₃O₄ nanoparticles have been incorporated into chitosan microparticles successfully and the particle size falls into the range of 164.05-768.69 nm. Their adsorption efficiencies for Cu (Ⅱ), Cd (Ⅱ) and Zn (Ⅱ) have been investigated, in which small size magnetic Fe₃O₄ loaded chitosan microparticles present higher adsorption efficiency than that of other ones. And their maximum adsorption capacity for Cu (Ⅱ), Cd (Ⅱ) and Zn (Ⅱ) could reach 51.66, 97.86 and 82.24% respectively. Moreover, the adsorbing mechanism can be well explained by pseudo-second-order model (R²=0.998-0.999). Notably, magnetic Fe₃O₄ loaded chitosan microparticles also exhibited excellent biocompatibility when co-cultured with MCF-7 cells with nearly 100% viability. This study demonstrates that small size magnetic Fe₃O₄ loaded chitosan microparticles is an effective, low cost and bio-compatible heavy metal adsorbent and could potentially be widely used in many different fields, for example, wastewater treatment in food and agriculture.