Molecules are the most demanding quantum systems to be simulated by quantum computers because of their complexity and the emergent role of quantum nature. The recent theoretical proposal of Huh et al. (Nature Photon., 9, 615 (2015)) showed that a multi-photon network with a Gaussian input state can simulate a molecular spectroscopic process. Here, we report the first experimental demonstration of molecular vibrational spectroscopy of SO$_{2}$ with a trapped-ion system. In our realization, the molecular scattering operation is decomposed to a series of elementary quantum optical operations, which are implemented through Raman laser beams, resulting in a multimode Gaussian (Bogoliubov) transformation. The molecular spectroscopic signal is reconstructed from the collective projection measurements on phonon modes of the trapped-ion system. Our experimental demonstration would pave the way to large-scale molecular quantum simulations, which are classically intractable.