Poly(3,4ethylenedioxythiophene):poly(4-styrenesulfonate) (PEDOT:PSS) has been intensively studied for its thermoelectric applications. Structural modulation to improve crystalline ordering, chain conformation and film morphology is a promising way to decouple the trade-off between conductivity and Seebeck coefficient and thus improve the thermoelectric power factor. Post treatment with ionic liquid ([CoCl2 ⋅ 6H2O]:[ChCl]) bearing cobalt-containing anions resulted in a remarkable enhancement of the power factor to 76.8 μW m−1 K−2. This IL combines the influence of a high-boiling polar organic solvent and diffusing ions. A high σ mainly resulted from the efficient removal of PSS chains, ordering of the structure and delocalization of bipoloran-dominant transport after conformational change. The increase in S was not due to dedoping of PEDOT chains, but rather the sharp feature of the density of states at the Fermi level induced by ion-exchange with unconventional anions.