This work presents a vulnerability assessment procedure for a complex structure using vibration characteristics. The structural behavior of a three-dimensional framed structure subjected to impact forces was predicted using the spectral element method. The Timoshenko beam function was applied to simulate the impact wave propagations induced by a high-velocity projectile at relatively high frequencies. The interactions at the joints were analyzed for both flexural and longitudinal wave propagations. Simulations of the impact energy transfer through the entire structure were performed using the transient displacement and acceleration responses obtained from the frequency analysis. The kill probabilities of the crucial components for an operating system were calculated as a function of the predicted acceleration amplitudes according to the acceptable vibration levels. Following the proposed vulnerability assessment procedure, the vulnerable positions of a three-dimensional combat vehicle with high possibilities of damage generation of components by impact loading were identified from the estimated vibration responses.