In this study, we demonstrated an idea of generating atomic-scale hologram of a molecule within one of its vibrational modes using X-ray holography. Hologram is recorded by incident X-ray wave, upon the molecule after triggering one of its vibrational modes. For simplicity, the ammonia (NH3) molecule is chosen as a test molecule while triggered in two distinct vibrational modes: the symmetric stretching and the scissoring modes. The result depicts that the vibrational dynamics modulate the holographic patterns, suggesting the way for developing a new technique of time-resolved molecular holography that captures both atomic position and vibrational state.