Epitaxial films of BaSi2 on Si(111) for solar cell applications possess three epitaxial variants and exhibit a minority carrier diffusion length (ca. 9.4 μm) much larger than the domain size (ca. 0.2 μm); thus, the domain boundaries (DBs) between the variants do not act as carrier recombination centers. In this work, transmission electron microscopy (TEM) was used to observe the atomic arrangements around the DBs in BaSi2 epitaxial films on Si(111), and the most stable atomic configuration was determined by first-principles calculations based on density functional theory to provide possible interface models. Bright-field TEM along the a-axis of BaSi2 revealed that each DB was a twin boundary between two different epitaxial variants, and that Ba(II) atoms form hexagons containing central Ba(I) atoms in both the bulk and DB regions. Four possible interface models containing Ba(I)-atom interface layers were constructed, each consistent with TEM observations and distinguished by the relationship between the Si tetrahedron arrays in the two domains adjacent across the interface. This study assessed the structural relaxation of initial interface models constructed from surface slabs terminated by Ba(I) atoms or from zigzag surface slabs terminated by Si tetrahedra and Ba(II) atoms. In these models, the interactions or relative positions between Si tetrahedra appear to dominate the relaxation behavior and DB energies. One of the four interface models whose relationship between first-neighboring Si tetrahedra across the interface was the same as that in the bulk was particularly stable, with a DB energy of 95 mJ/m2. There were no significant differences in the partial densities of states and band gaps between the bulk and DB regions, and it was therefore concluded that such DBs do not affect the minority carrier properties of BaSi2.