Conductive thiophene-based polymers have garnered great attention for use in organic electron materials such as electrochromic and thermoelectric materials. However, they suffer from poor electron transport properties and long-term stability, leading to 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 at the thiophene ring effectively achieved a large increase in the electrical conductivity with nearly invariable Seebeck coefficient, resulting in an enhancement by 1 order of magnitude for the 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.