Abstract: Problems resulting from the emission of crude oil, toxic organic solvents, and petroleum products, as well as massive heat dissipation from industrial pipes, have threatened ecosystems, human health, and industrial production. Eco-friendly and biodegradable natural materials are considered as the most promising absorbents or thermal insulation materials for oil–water separation and thermal insulation. In this work, agarose nanowire aerogels (ANAs) prepared from agarose (AG) solution were synthesized without any chemical reaction or chemical crosslinking agents to form AG hydrogels followed by supercritical CO2 (SC-CO2) drying. Then, hydrophobic agarose nanowire aerogels (HANAs) were obtained through a simple chemical vapor deposition (CVD) approach using methyltrimethoxysilane and methyltrichlorosilane. The gel skeleton of the HANAs after CVD was isometrically covered by a rigid silica coating with methyl on the ANA surface to improve flexibility, resulting in not only excellent self-cleaning and hydrophobicity with a water contact angle of 142° but also outstanding elasticity. Furthermore, the as-synthesized HANAs exhibited low density (≤0.09 g/cm3), a large specific surface area (≥210.5 m2/g), and high porosity (94.9–98.7%). Hence, the HANAs displayed high absorption capacities (approximately 48.2 g/g of chloroform absorption capacity) and selectivity of oils and organic solvents. In addition, they also exhibited excellent thermal insulation performance under both hot and cold conditions. The designed HANAs are expected to provide a highly efficient method for oil–water separation and thermal insulation.