AbstractQuantum phononic systems have attracted great attention in quantum science and technology. However, it is quite difficult to realize strong phonon–phonon interactions at the few phonon level in phononic systems, since direct interactions between phonons are generally very weak. Here, the phonon transport properties and the phonon–phonon interactions in a 1D phononic waveguide with embedded silicon‐vacancy (SiV) centers are studied. The authors show that, mediated by the SiV centers, strong phonon–phonon interactions can be realized due to coherent interferences of the emitting phonon waves with the incident waves. In particular, the embedded color centers can induce an effective attractive or repulsive interaction in space for phonons, corresponding to phonon bunching or antibunching. Besides, it is found that a single SiV center can capture two resonant phonons simultaneously, forming a phononic bound state in the continuum. Comparing with photon–photon interactions in photonic systems, the phonon–phonon interactions are stronger for relatively slower phonon velocity and the strongly correlated phonon properties are promising for constructing various all‐phonon quantum devices in quantum information processing.