To study the projectile structural response frequency characteristic, through established finite element model of the projectile, the natural frequencies and mode shapes of the projectile is solved using the projectile structural modal analysis. And resonance frequency which is under penetration resistance is obtained using the harmonic response analysis. Penetration acceleration signal is non-stationary and time varying. In order to accurately estimate the corresponding frequency response of the structure of the missile body, ensemble empirical mode decomposition algorithm is used to analyze penetration acceleration signal and find a component which corresponds to the harmonic response analysis resonant frequency. Through analysis the measured penetration four-tiers concrete target acceleration signals, the IMF3 (the third intrinsic mode functions) component frequency is consistent with the natural frequency of projectile structural response income by harmonic response analysis and frequency error is 4.2%. So the IMF3 component is projectile structural response of the acceleration signal and obtains the frequency of projectile structure response.