Phonon modes play a vital role in the cooperative phenomenon of light-induced spin transitions in spin crossover (SCO) molecular complexes. Although the cooperative vibrations, which occur over several hundreds of picoseconds to nanoseconds after photoexcitation, are understood to play a crucial role in this phase transition, they have not been precisely identified. Therefore, we have performed a novel optical laser pump-nuclear resonance probe experiment to identify the Fe-projected vibrational density of states (pDOS) during the first few nanoseconds after laser excitation of the mononuclear Fe(II) SCO complex [Fe(PM-BiA)2(NCS)2]. Evaluation of the so obtained nanosecond-resolved pDOS yields an excitation of ∼8% of the total volume of the complex from the low-spin to high-spin state. Density functional theory calculations allow simulation of the observed changes in the pDOS and thus identification of the transient inter- and intramolecular vibrational modes at nanosecond time scales.