A thermal protection system (TPS) is designed and fabricated to protect a hypersonic vehicle from extreme conditions. Good condition of the TPS panels is necessary for the next flight mission. A loose bolted joint is a crucial defect in a metallic TPS panel. This study introduces an experimental method to investigate the dynamic characteristics and state of health of a metallic TPS panel through an operational modal analysis (OMA). Experimental investigations were implemented under free-free supports to account for a healthy state, the insulation effect, and fastener failures. The dynamic deformations resulted from an impulse force were measured using a non-contact three-dimensional point tracking (3DPT) method. Using changes in natural frequencies, the damping ratio, and operational deflection shapes (ODSs) due to the TPS failure, we were able to detect loose bolted joints. Moreover, we also developed an in-house program based on a modal assurance criterion (MAC) to detect the state of damage of test structures. In a damage state, such as a loose bolted joint, the stiffness of the TPS panel was reduced, which resulted in changes in the natural frequency and the damping ratio. The calculated MAC values were less than one, which pointed out possible damage in the test TPS panels. Our results also demonstrated that a combination of the 3DPT-based OMA method and the MAC achieved good robustness and sufficient accuracy in damage identification for complex aerospace structures such as TPS structures.