The experimental results on the synthesis of flexible and superhydrophobic silica aerogels using methyltrimethoxysilane (MTMS) precursor by a two-step (acid–base) sol–gel process followed by the supercritical drying are reported. The effects of various sol–gel parameters on the flexibility of the aerogels have been investigated. The aerogels of different densities were obtained by varying the molar ratio of MeOH/MTMS(S) from 14 to 35, with lower densities for larger S values. It has been observed that the Young’s modulus (Y) decreased from 14.11 × 10⁴ to 3.43×10⁴ N/m² with the decrease in the density of the aerogels from 100 to 40 kg/m³. Simultaneously, the aerogels are superhydrophobic with a contact angle as high as 169^◦. The superhydrophobic aerogels are thermally stable up to a temperature of 463 K, above which they become hydrophilic. The aerogels have been characterized by bulk density, percentage volume shrinkage, and porosity measurements. The microstructures of the aerogels have been studied using the transmission electron microscopy (TEM). The Young’s modulus of the aerogels has been determined by an uniaxial compression test. The variation of physical properties of the aerogels has been explained by taking into consideration the hydrolysis, condensation reactions, the resulting colloidal clusters and their network formation.