As naturally derived material, cellulose aerogels have excellent thermal insulation properties due to their unique high porosity and three-dimensional mesoporous structure. However, its hydrophilic properties limit its application in the field of building insulation. Here, we propose a method to prepare high hydrophobicity by adopting the sol-gel method and chemical vapor reaction strategy using cellulose acetate type II as raw material and 2,4-toluene diisocyanate as the cross-linking agent. Thermal properties of cellulose acetate aerogels (CAAs) were measured, where pyridine was the catalyst, acetone was the solvent, and perfluorodecyltriethoxysilane (PFDS), hexamethyldisilazane (HMDS), and methyltriethoxysilane (MTES) were used as hydrophobic agents (by process hydrophobic test). Compared with MTES-modified cellulose acetate aerogels (M-CAAs) and HMDS (H-CAAs)-modified cellulose acetate aerogels, PFDS-modified (P-CAAs) cellulose acetate aerogels are the most hydrophobic. By implementing hydrophobic modification of PFDS both inside and outside the structure of cellulose acetate aerogels, the water contact angle can reach up to 136°, strongly demonstrating the potential of PFDS as a hydrophobic agent. The results show that the thermal conductivity and compressive strength of cellulose acetate aerogel with the best hydrophobic properties are 0.035 W m⁻¹ K⁻¹ at normal pressure and 0.39 MPa at 3% strain, respectively. This work shows that the highly hydrophobic cellulose acetate aerogel has potential as a waterproof material in the field of building thermal-insulation materials.