Low density aerogels with high fatigue resistance are widely used in the manufacturing of core material structures in aircraft fuselage to be able to tolerate the extreme environment of aerospace. However, most organic aerogel materials have poor energy absorption of external impact forces, and are prone to irreversible deformation, such as contracture and collapse in the process of long-term service. In order to solve this problem, a new type of thermosetting-thermoplastic polyimide composite aerogel was prepared, with its microstructure presenting the coexistence of the inner and outer skeletons. The intermolecular forces promoted the assembly of the soft thermoplastic layer and the strong thermosetting layer in the thermodynamic process with 4.63–6.55 μm range. The hard-soft layer structure improved the compressive and the shear load bearing capacities by bending of the panel (Compressive modulus is 1.60 MPa–3.52 MPa, tensile modulus is 1.04 MPa–1.45 MPa). Its permanent degradation less than 1.5 % after 500 cycles at 30 % strain. C–CPIAs also exhibited excellent heat resistance and thermal insulation performances, with a T5% value of 612 °C (C-CPIA-2), Tg of 458 °C (C-CPIA-3). The sandwich materials can be used as outer protective composite material of aircraft fuselage for future deep space missions.