Aerogels are a kind of porous materials with three-dimensional network structures, which possess extremely low density, large specific surface area, high porosity, and low thermal conductivity. Under the promotion of sustainability, aerogels derived from bagasse have been developing. In this report, hydrophobic bagasse aerogels were facilely prepared in an environmental-friendly strategy, including milling of bagasse, mixing with AKD emulsion, freeze drying and thermo-crosslinking. The optimal hydrophobic bagasse aerogel was obtained at an AKD content of 10 wt% and a slurry consistency of 3 wt%, whose density, porosity and WCA was 47.3 mg cm–3, 95.9% and 148°, respectively. It exhibited a high oil absorption capacity (31.65 g g–1) and a low thermal conductivity (36.28 mW m–1K–1), which could be applied for oil/water or emulsion separation and thermal insulation. The fabrication method would provide a novel idea for other bio-based hydrophobic aerogels.