A dynamic matrix of rare-gas crystals is constructed within the model of deformable and polarizable atoms based on the nonempirical short-range repulsion potential taking into account the three-body interaction and deformation of electron shells of dipole-type atoms within the pair and three-body approximations. Ab initio calculations of the phonon energy for compressed rare-gas crystals are performed at two and ten mean-value points of the Chadi–Kohen method in a wide pressure range. It is shown that the contribution of three-body forces to the phonon frequencies due to overlap of electron shells of neighboring atoms is small as compared to the pair interaction even at a high pressure and most pronounced for Xe. The contributions of the deformation of electron shells within the pair and three-body approximations differ for different mean-value points and increase with an increase in pressure. The zero-point energies calculated by the Chadi–Kohen method for crystals of the Ne–Xe series are compared with the known experimental data at p = 0 and calculation results obtained by other researchers.