The work unravels the previously unexplored atomic-scale mechanism involving the interaction of phonons with crystal homointerfaces. Silicon nanowires with engineered isotopic content and crystal phases were chosen for this investigation. Crystal polytypism, manifested by the presence of both diamond cubic and rhombohedral phases within the same nanowire, provided a testbed to study the impact of phase homointerfaces on phonon transport. The lattice thermal conductivity and its temperature response were found to be markedly different in the presence of polytypism. Its origin, however, was not traced to any acoustic mismatch as the polytypic nanowires presented a similar phonon spectrum as their counterparts. Rather, phenomenological modeling and atomistic simulations identified and quantified the role of atomically rough homointerfaces and the subsequent phonon scattering from such homointerfaces in shaping the phonon behavior. This framework provides the inputs necessary to advance the design and modeling of phonon transport in nanoscale semiconductors.