We investigated the structural and thermoelectric properties poly(3,4-ethylenedioxythiophene) (PEDOT) films with several dopants (counter ions, ClO4, PF6, and BF4), synthesised by electropolymerization. We first performed cyclic voltammetry analysis to determine the optimum synthesis conditions of the PEDOT thin films. We found that the surface morphology of the PEDOT thin films was dependent on the type of the dopant. The PF6-doped PEDOT (PEDOT:PF6) thin films showed a dense structure, and the PEDOT:ClO4 thin films showed a highly porous microstructure. Fourier transform infrared (FT-IR) spectroscopy showed that all the PEDOT thin films showed similar chemical structures and the p-type state. Regarding their thermoelectric properties, the electrical conductivity of the all the doped PEDOT thin films increased as the dopant concentration increased, with the PEDOT:PF6 thin films showing the highest value. On the other hand, the Seebeck coefficient of the PEDOT thin films with all the dopants decreased as the dopant concentration increased, with the PEDOT:BF4 thin films achieving the highest value. As a result, the PEDOT:BF4 thin films exhibited the highest power factor of 0.75 µW/(m·K2) at a dopant concentration of 1.0 M. We think that the PEDOT microstructure produced using the different types of dopant may affect the thermoelectric properties.