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Abstract Engineering of phonons, that is, collective lattice vibrations in crystals, is essential for manipulating physical properties of materials such as thermal transport, electron‐phonon interaction, confinement of lattice vibration, and optical polarization. Most approaches to phonon‐engineering have been largely limited to the high‐quality heterostructures of III–V compound semiconductors. Yet, artificial engineering of phonons in a variety of materials with functional properties, such as complex oxides, will yield unprecedented applications of coherent tunable phonons in future quantum acoustic devices. In this study, artificial engineering of phonons in the atomic‐scale SrRuO₃/SrTiO₃superlattices is demonstrated, wherein tunable phonon modes are observed via confocal Raman spectroscopy. In particular, the coherent superlattices led to the backfolding of acoustic phonon dispersion, resulting in zone‐folded acoustic phonons in the THz frequency domain. The frequencies can be largely tuned from 1 to 2 THz via atomic‐scale precision thickness control. In addition, a polar optical phonon originating from the local inversion symmetry breaking in the artificial oxide superlattices is observed, exhibiting emergent functionality. The approach of atomic‐scale heterostructuring of complex oxides will vastly expand material systems for quantum acoustic devices, especially with the viability of functionality integration.