Conducting polymer based thermoelectric systems are very effective at harvesting electricity from waste heat with low-temperature gradients relative to environmental temperature. However, although various studies concerning the doping effect exist, there are insufficient reports on the effect of the change in polymer chain structure on the thermoelectric properties. Here we demonstrate different poly(3,4-ethylene dioxythiophene) (PEDOT)-derivative chain structures (such as linear, two-dimensional, co-polymer), by varying the amount of three-armed conjugated cross-linker (1,3,5-tri(2-thienyl)-benzene (TTB)). At a small amount of TTB addition (until 0.5 mM), the electrochemical charge transport of the PEDOT films increased without shift of the UV–Vis absorbing property. However, from higher than 0.5 mM TTB, electrochemical charge transport decreased with blue shift of the UV–Vis absorbing curve. Moreover, the power factor of the PEDOT-derivative films without TTB to a small amount of TTB (0.5 mM) was improved from (27.03 to 49.43) µW m-1 K-2, and at higher than 0.5 mM TTB concentration, was diminished, respectively, because a small amount of TTB enhanced the π-π interaction of the polymer chains without disrupting the conjugation, while excess TTB molecules blocked conjugation of the polymer.