Density functional theory (DFT) calculations of protonated methanol–water mixed clusters, H⁺(MeOH)₁(H₂O)_n (n = 1–8), were extensively carried out to analyze the hydrogen bond structures of the clusters. Various structural isomers were energy optimized, and their relative energies with zero point energy corrections and temperature dependence of the free energies were examined. Coexistence of different morphological isomers was suggested. Infrared spectra were simulated on the basis of the optimized structures. The infrared spectra were also experimentally measured for n = 3–9 in the OH stretching vibrational region. The observed broad bands in the hydrogen-bonded OH stretch region were assigned in comparison with the simulations. From the DFT calculations, the preferential proton location was also investigated. Clear correlations between the excess proton location and the cluster morphology were found.