We report the results of experimental and theoretical studies of phonon modes in GaN/AlN superlattices (SLs) with a period of several atomic layers, grown by submonolayer digital plasma-assisted molecular-beam epitaxy, which have a great potential for use in quantum and stress engineering. Using detailed group-theoretical analysis, the genesis of the SL vibrational modes from the modes of bulk AlN and GaN crystals is established. Ab initio calculations in the framework of the density functional theory, aimed at studying the phonon states, are performed for SLs with both equal and unequal layer thicknesses. The frequencies of the vibrational modes are calculated, and atomic displacement patterns are obtained. Raman spectra are calculated and compared with the experimental ones. The results of the ab initio calculations are in good agreement with the experimental Raman spectra and the results of the group-theoretical analysis. As a result of comprehensive studies, the correlations between the parameters of acoustic and optical phonons and the structure of SLs are obtained. This opens up new possibilities for the analysis of the structural characteristics of short-period GaN/AlN SLs using Raman spectroscopy. The results obtained can be used to optimize the growth technologies aimed to form structurally perfect short-period GaN/AlN SLs.