The poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) composite has been gaining attention as a potential organic thermoelectric material owing to its superior electrical property and low thermal conductivity. Several experiments have recently demonstrated that introduction of high-boiling-point solvents increases optimal charge carrier concentration and leads to high crystallinity, resulting in noticeable improvement of thermoelectric performance. Therefore, much attention has been paid to electrical properties. Understanding of intrinsic heat conduction in PEDOT is also important since the thermal conductivity of bulk polymers is sensitive to macroscopic alignment and transport properties of individual chains. Moreover, thermoelectric performance inversely scales with thermal conductivity. In this work, by molecular dynamics simulations, we have investigated heat conduction in PEDOT chains and evaluated the impact of adsorbed protonic acid on the thermal conductivity of PEDOT. Owing to the quasi-ballistic nature of heat conduction in PEDOT chains, we found that thermal conductivity has strong size dependence and varies from 1–10 W m−1 K−1. Furthermore, we found that the adsorption on PEDOT of toluene sulfonic acid (TSA); a monomer of PSS; suppresses contribution of the long-wavelength phonons to heat conduction. These results suggest that decreasing the length of PEDOT chains in a composite and increasing the surface density of adsorbed TSA molecules are effective methods of reducing the thermal conductivity of the composite, leading to the enhancement of thermoelectric performance.