Owing to the high flexibility, low thermal conductivity, and tunable electrical transport property, poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) exhibits promising potential for designing flexible thermoelectric devices in the form of films or fibers. However, the low Seebeck coefficient and power factor of PEDOT:PSS have restricted its practical applications. Here, we sequentially employ triple post-treatments with concentrated sulfuric acid (H2SO4), sodium borohydride (NaBH4), and 1-ethyl-3-methylimidazolium dichloroacetate (EMIM:DCA) to enhance the thermoelectric performance of flexible PEDOT:PSS fibers with a high power factor of (55.4 ± 1.8) μW m-1 K-2 at 25 °C. Comprehensive characterizations confirm that excess insulating PSS can be selectively removed after H2SO4 and EMIM:DCA treatments, which induces conformational changes to increase charge carrier mobility, leading to enhanced electrical conductivity. Simultaneously, NaBH4 treatment is employed to adjust the oxidation level, further optimizing the Seebeck coefficient. Additionally, the assembled flexible fiber thermoelectric devices show an output power density of (60.18 ± 2.79) nW cm-2 at a temperature difference of 10 K, proving the superior performance and usability of the optimized fibers. This work provides insights into developing high-performance organic thermoelectric materials by modulating polymer chains.