The structure–property relationship at interfaces is difficult to probe for thermoelectric materials with a complex interfacial microstructure. Designing thermoelectric materials with a simple, structurally‐uniform interface provides a facile way to understand how these interfaces influence the transport properties. Here, we synthesized Bi2−xSbxTe3 (x = 0, 0.1, 0.2, 0.4) nanoflakes using a hydrothermal method, and prepared Bi2−xSbxTe3 thin films with predominantly (0001) interfaces by stacking the nanoflakes through spin coating. The influence of the annealing temperature and Sb content on the (0001) interface structure was systematically investigated at atomic scale using aberration‐corrected scanning transmission electron microscopy. Annealing and Sb doping facilitate atom diffusion and migration between adjacent nanoflakes along the (0001) interface. As such it enhances interfacial connectivity and improves the electrical transport properties. Interfac reactions create new interfaces that increase the scattering and the Seebeck coefficient. Due to the simultaneous optimization of electrical conductivity and Seebeck coefficient, the maximum power factor of the Bi1.8Sb0.2Te3 nanoflake films reaches 1.72 mW m−1 K−2, which is 43% higher than that of a pure Bi2Te3 thin film.