Deeply understanding the physical and chemical properties of a melt requires an accurate description of its structure. In this paper, we investigated the structures of Li₄GeO₄ and Li₆Ge₂O₇ melts which are of interest for growing germanate functional crystals. The structural changes of polycrystalline Li₄GeO₄ and Li₆Ge₂O₇ from room temperature to their melting temperatures were monitored by Raman spectroscopy and analyzed by density functional theory (DFT) and factor group theory (FGT) calculations. A striking spectral change was observed for polycrystalline Li₄GeO₄, which is due to the orthorhombic-to-monoclinic phase transition and the Li⁺ disorder induced by the phase transition. Spectral similarity between monoclinic Li₄GeO₄ and its corresponding melt indicates that the anion motif of the Li₄GeO₄ melt is the GeO₄⁴⁻ tetrahedron. The Li₆Ge₂O₇ crystal has 180 lattice phonons (45A_g + 45A_u + 45B_g + 45B_u) at the centre of the Brillouin zone, including 90 Raman-active phonons (45A_g + 45B_g). All the Raman-active bands were assigned by DFT calculations. The Raman spectrum of polycrystalline Li₆Ge₂O₇ varies smoothly and continuously in the heating/melting process, indicating that the Ge₂O₇⁶⁻ anion groups in the crystal are preserved in the melt. The disproportionation reaction that often occurs in silicate melts was not found in the Li₆Ge₂O₇ melt. A nucleophilic substitution reaction is proposed to explain the composition-induced structural transformation present in the Li⁺-rich germanate melts.