We first reported the simultaneous in-situ amine-modification and hydrophobization of a native silica aerogel at the benign temperature of 0°C for further isocyanate cross-linking, compared with the traditional method at the harsh temperature of −77°C. The hydrolysis of tetraethylorthosilicate (TEOS) was slower than that of tetramethoxysilane (TMOS) and each methyltrimethoxysilane (MTMS) monomer had one non-hydrolyzable methyl group. The hydrophobicity of the native silica aerogels could be adjusted by tunning the MTMS/TEOS molar ratio. The 3-aminopropyltriethoxysilane (APTES) was used to provide a flexible linking group in the silica structure, while the amine group in APTES was further used as a reactive site for reacting with the isocyanate. As a result, a lightweight, mechanically strong and porous silica-based composite material was obtained by encapsulating the skeletal framework of amine-modified silica aerogels with isocyanate.