Multilayer thin film structuring offers a versatile strategy to tailor nanostructures through interface engineering. Atomic layer deposition (ALD) provides precise control of composition and structure via supercycle approaches that enable the multiple metal species introduction. However, the resulting growth behavior is often interpreted without fully accounting for interfacial effects that govern nucleation and nanostructure evolution. In this work, we demonstrate that introducing SnSe₂ layers into Sb₂Te₃/SnSe₂ multilayer films using ALD supercycle significantly enhances Sb₂Te₃ nucleation and accelerates out-of-plane growth, leading to an increase in growth per cycle (GPC) from 0.18 to 0.69 Å/cycle. First-principles atomistic simulations of precursor deposition chemistry and extremely surface-sensitive low-energy ion scattering (LEIS) analysis confirm the promoted growth of Sb₂Te₃ in Sb₂Te₃/SnSe₂ multilayer structures, which is also accompanied by elemental exchange reactions between Te and Se atoms. The resulting Sb₂Te₃/SnSe₂ multilayer thin films exhibit increased charge carrier and phonon scattering, leading to a significant reduction in lattice thermal conductivity from 1.09 to 0.25 W/mK at room temperature due to the modulated nanostructure. This study establishes a robust analytical framework for understanding and engineering interfacial reactions and nucleation phenomena in ALD-based multilayer systems.