In order to investigate the relationship between thermoelectric properties and chemical structures of conducting polymers, electrochemically-doped polythiophenes partially substituted by ethylenedioxy groups have been synthesized and their thermoelectric properties were measured. Two types of monomers consisting of 3,4-ethylenedioxythiophene (EDOT) and 3-hexylthiophene (HT) with different mole fractions of EDOT have been synthesized. The electrolytic polymerization of these monomers in propylene carbonate solutions containing sulfonated poly(β-hydroxyether) (S-PHE) as an electrolyte gave smooth and lustrous free-standing films. The electrical conductivities and Seebeck coefficients of the polymer films doped with S-PHE were increased with the increase in the temperature or the decrease in the current density during the electrolytic polymerization. By the comparison of thermoelectric properties of S-PHE doped polymer films, it was revealed that the thermoelectric performances were strongly affected by the mole fractions of EDOT in the copolymers.