To help understand the factors controlling the performance of one of the most promising n-type oxide thermoelectric SrTiO3, we need to explore structural control at the atomic level. In Sr1–xLa2x/3TiO3 ceramics (0.0 ≤ x ≤ 0.9), we determined that the thermal conductivity can be reduced and controlled through an interplay of La-substitution and A-site vacancies and the formation of a layered structure. The decrease in thermal conductivity with La and A-site vacancy substitution dominates the trend in the overall thermoelectric response. The maximum dimensionless figure of merit is 0.27 at 1070 K for composition x = 0.50 where half of the A-sites are occupied with La and vacancies. Atomic resolution Z-contrast imaging and atomic scale chemical analysis show that as the La content increases, A-site vacancies initially distribute randomly (x < 0.3), then cluster (x ≈ 0.5), and finally form layers (x = 0.9). The layering is accompanied by a structural phase transformation from cubic to orthorhombic and the formation of 90° rotational twins and antiphase boundaries, leading to the formation of localized supercells. The distribution of La and A-site vacancies contributes to a nonuniform distribution of atomic scale features. This combination induces temperature stable behavior in the material and reduces thermal conductivity, an important route to enhancement of the thermoelectric performance. A computational study confirmed that the thermal conductivity of SrTiO3 is lowered by the introduction of La and A-site vacancies as shown by the experiments. The modeling supports that a critical mass of A-site vacancies is needed to reduce thermal conductivity and that the arrangement of La, Sr, and A-site vacancies has a significant impact on thermal conductivity only at high La concentration.