Understanding and controlling the growth of chalcogenide perovskite thin films through interface design is important for tailoring film properties. Here, the film and interface structure of BaZr(S,Se)3 thin films grown on LaAlO3 by molecular beam epitaxy and postgrowth anion exchange is resolved using aberration-corrected scanning transmission electron microscopy. Epitaxial films are achieved from self-assembly of an interface “buffer” layer, which accommodates the large film/substrate lattice mismatch of nearly 40% for the alloy film studied here. The self-assembled buffer layer, occurring for both the as-grown sulfide and post-selenization alloy films, is shown to have rock-salt-like atomic stacking akin to a Ruddlesden–Popper phase. These results provide insights into oxide-chalcogenide heteroepitaxial film growth, illustrating a process that yields relaxed, crystalline, epitaxial chalcogenide perovskite films that support ongoing studies of optoelectronic and device properties.