AbstractIsotopic mixtures result in distinct properties of materials such as thermal conductivity and nuclear process. However, the knowledge of isotopic interface remains largely unexplored mainly due to the challenges in atomic-scale isotopic identification. Here, using electron energy-loss spectroscopy in a scanning transmission electron microscope, we reveal momentum-transfer-dependent phonon behavior at the h−¹⁰BN/h-¹¹BN isotope heterostructure with sub-unit-cell resolution. We find the phonons’ energy changes gradually across the interface, featuring a wide transition regime. Phonons near the Brillouin zone center have a transition regime of ~3.34 nm, whereas phonons at the Brillouin zone boundary have a transition regime of ~1.66 nm. We propose that the isotope-induced charge effect at the interface accounts for the distinct delocalization behavior. Moreover, the variation of phonon energy between atom layers near the interface depends on both of momentum transfer and mass change. This study provides new insights into the isotopic effects in natural materials.