Extra bilirubin in the blood can provoke serious illness in patients with severe liver disease. Hemoperfusion is an effective method to remove the extra bilirubin, but its application is limited by the low adsorption efficiency and poor biocompatibility of available adsorbent materials. In this study, chitin/ordered mesoporous carbon CMK3 (Ch/CMK3) microspheres are successfully prepared. Results of characterization experiments indicated that these composite microspheres possess a multilayered porous nanofibrous structure with an extremely large specific surface area (300.19 m 2 g −1 ) and large pore size. Notably, the Ch/CMK3 microspheres demonstrated a high bilirubin adsorption capacity (228.19 mg g −1 ) in phosphate buffer solution (PBS), and an outstanding bilirubin removal ratio (76.78% ± 4.40%) in the plasma of rabbits with hyperbilirubinemia without affecting the protein components. More importantly, the Ch/CMK3 microspheres showed no effect on other blood components, no cytotoxicity, and no systemic toxicity to mice. Cell co-culture experiments revealed that the microspheres can provide a 3-dimensional (3D) space to promote cell adhesion, proliferation, and nutrient exchange. These Ch/CMK3 microspheres featuring a strong ability for bilirubin adsorption and good biocompatibility can be a promising candidate in biomedical applications such as hemoperfusion, cell microcarrier, and 3D tissue engineering.