Abstract Underground frame structure is an important structure form of civil air defense engineering, and its damage diagnosis is an important link in safety evaluation of civil air defense engineering. Based on the analysis of the dynamic properties of underground frame structure before and after damage, it was proved that modal strain energy was sensitive to damage of element. Therefore, the variation rate of element modal strain energy was taken as the signature for damage detection, and it was proved that the variation of element modal strain energy caused by multiple damage state was transformed into superposition of single damage state. The combined optimization method was proposed to resolve damage detection of multiple damages of civil air defense structure. A typical civil air defense engineering was studied as an example. Calculation results under different damage situation are analyzed and discussed. It is revealed that the proposed method is effective, and it not only can identify the damages in structure with high precision, but also can simply the process of damage diagnosis.