ABSTRACT BST/WSe 2 heterostructures are deposited via pulsed laser deposition to examine the influence of interfacial structure and compositional heterogeneity on thermoelectric performance. X‐ray diffraction reveals high crystallinity with uniform lattice compression along both in‐plane and out‐of‐plane directions, accompanied by minor secondary phase inclusions. Cs‐STEM resolves well‐defined quintuple layers and compressed van der Waals gaps. At the same time, lattice strain is evident in structurally distorted regions, and moiré patterns arising from lattice mismatch are specifically observed within the mixed region adjacent to the BST interfaces. Temperature‐dependent transport measurements show enhanced electrical conductivity, with S3 reaching the highest values and S2 closely following, driven by thermally activated carrier generation. Positive Seebeck coefficients indicate p‐type transport, with S2 maintaining >430 µV K −1 from 310 to 440 K due to interfacial energy filtering. Non‐uniform WSe 2 domains form internal p–n junction‐like regions that locally tune carrier concentration and reinforce energy filtering. Effective mass analysis suggests band flattening due to interfacial strain and moiré reconstruction, enabling high Seebeck coefficients and thermally stable power factor (>50 µW cm −1 K −2 ).