Conductive thiophene-base polymers have gained great concern in the organic electron materials such as electrochromic and thermoelectric materials. However, they suffer from poor electron transport property and long-term stability leading to the limited development eventually. Here, we proposed a strategy of functionalized thiophene-based polymers with oligo(ethylene glycol) or alkyl side chains and synthesized a series of poly(3,4-ethylenedioxy bithiophene)s (PEDTs) to tune their electrochromic and thermoelectric properties. An alkyl group bearing electronic ability in thiophene ring effectively achieved a large increase in the electrical conductivity with nearly invariable Seebeck coefficient resulting in an enhancement by one order of magnitude for thermoelectric power factor. Moreover, the electrochromic properties of functionalized PEDTs gained an effective improvement in the optical contrast and coloration efficiency as well as stability with multicolor changes between neutral and oxidized states. The functionalized PEDTs can be proposed as an alternative strategy to tune the electrochromic and thermoelectric properties for organic polymer materials.