Silica aerogel was often reinforced with glass fiber and changed to hydrophobicity via a surface modification to overcome its fragile and hygroscopic nature for practical application. However, though the mechanical and hydrophobic performances of the silica aerogel were improved, its unique ultra-low thermal conductivity was compromised. In order to prepare the hydrophobic silica aerogel felt while maintaining its excellent mechanical and insulation performances, the tetraethoxysilane and methyltrimethoxysilane (MTMS) as co-precursors, glass fiber as felt, and silica gel as a filling agent were selected to make the felt. An approach of the two-step sol–gel process followed by supercritical CO2 drying was applied. The morphology, structure, and properties of the felt were analyzed by field emission scanning electron microscope, a Fourier transform infrared spectrometer, and a thermal constants analyzer, etc. It was found that the felt showed excellent mechanical, thermally insulating, and hydrophobic performance. Also, it maintained low density and had higher thermal stability, due to the addition of silica gel and MTMS in the felt. The former enhanced the combination of silica aerogel with glass fiber and improved the microstructure of the felt. The latter endowed the felt excellent hydrophobicity, flexibility, and thermal stability.