The structure of binary glasses xMgO·(1−x)P2O5 (x = 0.30, 0.35, 0.40, 0.45, 0.50, and 0.55) was studied by thermodynamic model (TDM) of Shakhmatkin and Vedishcheva (SV) and Raman spectroscopy. In the TDM, six following system components were considered: MgO (M), P2O5 (P), MgO·2P2O5 (MP2), MgO·P2O5 (MP), 2MgO·P2O5 (M2P), 3MgO·P2O5 (M3P). The principal component analysis (PCA) of experimental Raman spectra resulted in three independent components. The baseline subtracted and thermally corrected Raman spectra were analyzed by the multivariate curve analysis (MCR) for three components. The MCR resulted in the Raman spectra and relative abundance of each component. The experimental spectra were reproduced by the MCR on the level of 99.9%. Correlation analysis attributed the MCR components to M2P, MP, and MP2. Then the Malfait’s decomposition was performed based on the TDM-SV equilibrium molar amounts of system components (MP2, MP, and M2P) resulting in partial Raman spectra (PRS). Normalized MCR loadings coincide with normalized PRS. Adjusted scores were reproduced with good accuracy equilibrium molar amounts of system components.