Thermoelectric oxide thin films are promising in chip cooling. The issues on the orientation of thin films are essential as they are related to the structures, morphologies, and thermoelectric properties. In this regard, the orientation modulation is conducted on La‐doped SrTiO3 thin films on (LaAlO3)0.3(Sr2TaAlO6)0.7 (LSAT) single crystal substrates. Layer‐by‐layer growth mode is found in (001)‐ and (110)‐ oriented thin films, resulting in few grain boundaries (GBs). In (111)‐oriented films, island growth mode leads to columnar grain boundaries that build up potential barriers for electrons to be strongly scattered and filtered, suppressing electron mobility and increasing effective mass. In addition, the GBs serve as oxygen vacancy diffusion paths when annealing, causing increased carrier concentration and lattice contraction. The weighted mobility of 71.9 cm2 V−1 s−1 and electrical conductivity of ≈600 S cm−1 are realized in the (001)‐oriented film at room temperature. Ultimately, outstanding power factor values of ≈569 µW m−1 K−2 (room temperature) and ≈791 µW m−1 K−2 (573 K) are successfully achieved, outperforming those in polycrystalline ceramics and (111)‐oriented films. This study systematically investigates the influence of grain boundaries and orientations on SrTiO3‐based thermoelectric films, which lays a solid foundation for improving thermoelectric performance in other oxide thin films.