New flexible methylsilsesquioxane (MSQ) aerogels have been facilely prepared by a sol–gel process with methyltrimethoxysilane (MTMS) and dimethyldimethoxysilane (DMDMS) as co-precursors, followed by surface modification and ambient pressure drying. The microstructure, mechanical properties and hydrophobicity of these MSQ aerogels after surface modifications of hexamethyldisiloxane (HMDSO) and/or hexamethyldisilazane (HMDS) were investigated in detail, and the applications of surface-modified MSQ aerogels in sound-absorbance, fast dye adsorption and oil/water separation were evaluated, respectively. The MSQ aerogels surface-modified by HMDS possess flexibility, elasticity and superhydrophobicity, and demonstrate good performance in the mentioned applications. The resultant MSQ aerogel used in sound-absorbance has high frequency (about 6 kHz) acoustic absorptivity of up to 80%, benefiting from its macroporous structure and porosity of 94%, and it also possesses intermediate frequency acoustic absorptivity (about 1 kHz) up to 80% owing to its elasticity. This MSQ aerogel can selectively separate oil from oil/water mixtures with high efficiency due to its superhydrophobicity and superlipophilicity, resulting from a lot of methyl groups, density as low as 0.12 cm3·g−1 and a water contact angle as high as 157°. This MSQ aerogel can be assembled to be a monolithic column applied for fast dye adsorption, and shows selective adsorption for anionic dyes and removal efficiency of methyl orange of up to 95%.