The transformation of the vibrational spectrum of Cu2Zn(Sn1−xGex)S4 single crystals over the entire composition range (0 ≤ x ≤ 1) is studied experimentally by low-temperature Raman scattering and photoluminescence spectroscopies, as well as theoretically in the framework of density functional theory (DFT). It is shown that unlike “classic” mixed binary II–VI and III–V compounds, which are characterized by either one- or two-mode behavior of spectra transformation upon composition variation, the vibrational modes of the quaternary semiconductor Cu2Zn(Sn1−xGex)S4 exhibit both types of behavior within the same alloy system. DFT calculations reveal that the two-mode transformation is in fact observed for the vibrational modes, which possess a very small dispersion across the Brillouin zone, that is typical for a molecular crystal. These modes are due to the “breathing” motion of sulfur within GeS4 and SnS4 tetrahedra. The effects of structural (positional) disorder of mixed crystals are analyzed based on Raman scattering as well as photoluminescence results.