Air‐stable, lightweight, and electrically conductive conjugated polymers have attracted significant attention for thermoelectric applications, especially in low‐temperature environments. However, their low carrier mobility has limited broader adoption. This study addresses this challenge by investigating the nanostructure of poly(3,4‐ethylenedioxythiophene) (PEDOT) thin films fabricated via oxidative chemical vapor deposition (oCVD) at various deposition temperatures. Through systematic control of the semi‐crystalline orientation and π–π stacking distance, a substantial enhancement in carrier mobility (23.58 ± 1.71 cm2 V−1 s−1) and electrical conductivity (6345 ± 210 S cm−1) is achieved. The thermoelectric power factor demonstrates a direct correlation with deposition temperature, achieving a maximum value of 112.57 ± 4.33 µW m−1 K−2. PEDOT thin films fabricated at higher deposition temperatures show minimal reductions in electrical conductivity as absolute temperature decreased, reflecting a lower resistivity ratio and extended metallic state, as indicated by the metal–insulator transition in the Zabrodskii plot. Incorporating the Seebeck coefficient into the parabolic energy band diagram revealed strong agreement between theoretical and experimental carrier mobility, while also indicating that the energy barrier for intercrystalline charge transport decreases as deposition temperature increases. The highly face‐on orientation and reduced π–π stacking distance in PEDOT thin films facilitate quasi‐1D conduction, thereby enhancing carrier mobility.