Chiral symmetry breaking of phonons plays an essential role in emergent quantum phenomena owing to its strong coupling to spin degree of freedom. However, direct experimental evidence of the chiral phonon–spin coupling is lacking. In this study, we report a chiral phonon–mediated interlayer exchange interaction in atomically controlled ferromagnetic metal (SrRuO3)–nonmagnetic insulator (SrTiO3) heterostructures. Owing to the unconventional interlayer exchange interaction, we have observed rotation of spins as a function of nonmagnetic insulating spacer thickness, resulting in a spin spiral state. The chiral phonon–spin coupling is further confirmed by phonon Zeeman effect. The existence of the chiral phonons and their interplay with spins along with our atomic-scale heterostructure approach unveil the crucial roles of chiral phonons in magnetic materials.