Bio-based aerogels have attracted much attention due to their biodegradability and excellent oil-water separation properties. However, the preparation of inexpensive green aerogels with high separation efficiency is still a great challenge. In this paper, low-density, high-adsorption capacity and superhydrophobic chestnut shell-based bio-aerogels were prepared by chemical cross-linking and chemical vapor deposition using agricultural and forestry waste chestnut shells as the precursor of aerogels to achieve high efficiency of oil-water separation and to achieve the goal of “treating waste with waste”. The covalent cross-linking of chestnut shell cellulose and cross-linking agent to form silicone-containing functional groups improved the pore structure, hydrophobicity and mechanical properties of chestnut shell cellulose, and under the action of capillary force, the oil was retained in the pores of the bio-aerogels, which achieved the selective adsorption of oil and organic solvents in the oil-water mixture, with a separation efficiency of more than 98%. After 10 cycles, the bio-aerogel still has good reusability. This eco-friendly and low-cost aerogel provides a practical method for resource conversion and recycling, as well as a green and innovative way for the treatment of oily wastewater.