The thermoelectric properties of semiconducting polymers are influenced by both the carrier concentration and the morphology that sets the pathways for charge transport. A combination of optical, morphological, and electrical characterization is used to assess the effect of the role of disorder on the thermoelectric properties of thin films of poly(3‐hexylthiophene) (P3HT) doped with 2,3,5,6‐tetrafluoro‐7,7,8,8‐tetracyanoquinodimethane (F4TCNQ). Controlled morphologies are formed by casting blends of regioregular (RR‐P3HT) and regiorandom (RRa‐P3HT) and then subsequently doped with F4TCNQ from the vapor phase. Optical spectroscopy and X‐ray scattering show that vapor phase doping induces order in the disordered regions of thin films and increases the long‐range connectivity of the film. The thermoelectric properties are assessed as a function of composition and it is shown that while the Seebeck coefficient is affected by structural ordering, the electrical conductivity and power factor are more strongly correlated with the long‐range connectivity of ordered domains.