Hemoperfusion is regarded as the most effective treatment for hyperbilirubinemia. The adsorbent play crucial important role for bilirubin removal. An ideal adsorbent should possess good biocompatibility as well as high bilirubin adsorption capacity. In this study, two natural polymers composed of chitin and collagen plus KH560 that served as a crosslinking agent were selected to fabricate chitin/collagen composite aerogels (CKC), and potentially used as efficient bilirubin adsorption. The fabricated CKC aerogels exhibited homogeneous, dense and nanoscale 3D-porous nanofibrous structures. And the CKC aerogels showed high adsorption capacity (209.62 ± 2.28 mg/g) for free bilirubin within 4 h. More important, dynamic adsorption experiment illustrated the adsorption capacity reached to 265.22 ± 4.77 mg/g, larger than that of static adsorption. The further tests manifested the CKC aerogels had excellent blood compatibility and no toxicity in vivo. This novel naturally-based aerogels were an economical, biocompatible and efficient adsorbent for the bilirubin removal, potentially providing new ideas for development of new adsorbents.