Silica aerogels, which are constructed with silica nanoparticles and numerous nanoscale pores, have many outstanding attributes, but they are usually brittle and hydrophilic. For the construction of a robust aerogel, the novel polyhedral oligomeric silsesquioxane (POSS) was introduced to prepare a series of aerogels possessing particles covered with elastic cushion to improve the mechanical property. The multialkoxy POSS, which possessed stiff Si-O-Si nanocages and flexible alkyl chains, was synthesized via thiol-ene click chemistry. After a facile and efficient approach, a partially ordered structure of SiO2 nanoparticles and organic elastic cushion would form spontaneously within the aerogels. With the POSS as the only precursor, several outstanding attributes were achieved in a single aerogel such as high specific surface area (SSA), high compression strength, high compression modulus, and noticeable compression flexibility. Meanwhile, the aerogel was superhydrophobic of which the contact angle (CA) was higher than 153°. Moreover, the potential application of oil-water separation is also presented.