With the frequent occurrence of offshore oil spills, the effective separation and treatment of oily wastewater are essential to the environment. In this work, the core-shell bioreactor (abbreviated as Fe3O4/MHNTs-CNF@aerogel) was prepared with a core composed of camphor leaf cellulose-based aerogels for loading microorganisms and a shell derived from hydrophobic silane-modified halloysite doping with Fe3O4 for selective absorption of oil and maganetic recycling. The core-shell-structured bioreactor Fe3O4/MHNTs-CNF@aerogel has excellent self-floating properties and can float on water for up to 100 days. The whole core-shell structure not only has excellent oil/water separation performance but also has good microbial degradation performance. By applying it in water containing 5% diesel for the biodegradation test, the biodegradation efficiency of Fe3O4/MHNTs-CNF@aerogel for diesel can reach 82.4% in 10 days. The efficiency was 20% higher than for free microorganisms, and it still had excellent degradation ability after three degradation cycles, with a degradation rate of over 75%. In addition, the result obtained from the study on environmental tolerance shows that Fe3O4/MHNTs-CNF@aerogel possessed a strong tolerance ability under different pH and salinity conditions. The Fe3O4/MHNTs-CNF@aerogel also has superior mechanical properties; i.e., nearly no deformation occurs at 30 kPa. Compared with those conventional oil/water separation materials which can only absorb or separate the oils for water with limited capacity and taking the risk of secondary contamination, our core-shell-structured bioreactor is capable of not only selectively absorbing oil from water through its hydrophobic shell but also degrading it into a nontoxic substance by its microorganism-loaded core, thus showing great potential for practical application in oily wastewater treatment.