Bi₂Te₃-based alloys are known to have outstanding thermoelectric properties. Although structure–property relations have been studied, still, detailed analysis of the atomic and nano-scale structure of Bi₂Te₃ thin film in relation to their thermoelectric properties remains poorly explored. Herein, highly-textured (HT) and single-crystal-like (SCL) Bi₂Te₃ films have been grown using pulsed laser deposition (PLD) on Si wafer covered with (native or thermal) SiO_x and mica substrates. All films are highly textured with c-axis out-of-plane, but the in-plane orientation is random for the films grown on oxide and single-crystal-like for the ones grown on mica. The power factor of the film on thermal oxide is about four times higher (56.8 μW·cm⁻¹·K⁻²) than that of the film on mica (12.8 μW·cm⁻¹·K⁻²), which is comparable to the one of the polycrystalline ingot at room temperature (RT). Reduced electron scattering in the textured thin films results in high electrical conductivity, where the SCL film shows the highest conductivity. However, its Seebeck coefficient shows a low value. The measured properties are correlated with the atomic structure details unveiled by scanning transmission electron microscopy. For instance, the high concentration of stacking defects observed in the HT film is considered responsible for the increase of Seebeck coefficient compared to the SCL film. This study demonstrates the influence of nanoscale structural effects on thermoelectric properties, which sheds light on tailoring thermoelectric thin films towards high performance.