Due to their low bulk density, high porosity, and functional performance, aerogels are ideal candidates for a variety of applications. However, their potential application in a variety of fields is limited by their time-consuming and costly complex fabrication process. In this study, electrospun 3-aminopropyltriethoxysilane-grafted polyimide (PI@APTES) nanofibers were used to construct nanofibrous aerogels (NFAs) via freeze-drying a dispersion of cross-linked-PI short fibers and a binder (PI@APTES), resulting in improved properties and functionalities. A highly siloxane cross-linked network structure was formed by hydrolysis and condensation reactions to generate stable nanofibrous aerogels. The obtained polyimide nanofibrous aerogels (PiNFAs) had a hierarchically three-dimensional (3D) microporous structure, high porosity (over 98%), tunable densities (10.6 ± 0.7–13.6 ± 0.2 mg cm–3), solvent resistance, superhydrophobicity (water contact angle over 163°), low thermal conductivity (as low as 33.2 mW m–1 K–1), and mechanical stability. These PiNFAs are promising candidates for potential applications in thermal insulation, lightweight construction, filtration, and sensors.