Aerogel-cored stitched sandwich composites (ACSSCs), which possess numerous desirable properties, are anticipated to become the preferred choice for next-generation integrated thermal protection systems (ITPSs) in high-speed vehicles. Despite the reinforcement provided by stitching, the ACSSC structures on vehicles’ outer surfaces remain vulnerable to damage resulting from the excessively high deformation and vibration that occur during high-speed flight. Accordingly, experimental tests were conducted to investigate the failure characteristics of ACSSCs under bending vibration conditions. The tests demonstrated that the ACSSC structures were prone to fatigue failure caused by vibration, which resulted in significant shear damage in the aerogel core. Furthermore, the study introduced a new method for indirectly characterizing the fatigue life of shear damage in the core. Finite element analysis was undertaken to elucidate the cause of the cracking near the bottom layer of the core. The results indicated that the crack location of the aerogel core was littered with the high stiffness and deformation of internal stitches.