Self-organized silicide nanowires are considered as building blocks of future nanoelectronics and have been intensively investigated. In nanostructures, the lattice vibrational waves (phonons) deviate drastically from those in bulk crystals, which gives rise to anomalies in thermodynamic, elastic, electronic, and magnetic properties. Hence a thorough understanding of the physical properties of these materials requires a comprehensive investigation of the lattice dynamics as a function of the nanowire size. We performed a systematic lattice dynamics study of endotaxial nanowires, forming the metastable, surface-stabilized phase, which are in-plane embedded into the Si(110) surface. The average widths of the nanowires ranged from 24 to 3 nm, and their lengths ranged from several micrometers to about 100 nm. The Fe-partial phonon density of states, obtained by nuclear inelastic scattering, exhibits a broadening of the spectral features with decreasing nanowire width. The experimental data obtained along and across the nanowires unveiled a pronounced vibrational anisotropy that originates from the specific orientation of the tetragonal unit cell on the Si(110) surface. The results from first-principles calculations are fully consistent with the experimental observations and allow for a comprehensive understanding of the lattice dynamics of endotaxial silicide nanowires.