Recently, organic conductive polymer/carbon nanoparticle thermoelectric (TE) composites or hybrids have received considerable attention due to their attractive structural and electrical characteristics. Here, flexible films of poly(3,4-ethylenedioxythiophene)-tosylate/acidified-single-walled carbon nanotube (PEDOT-Tos/a-SWCNT) composites with greatly enhanced TE performance are fabricated by combination of chemical oxidative polymerization, acid-treatment of SWCNT and vacuum filtration. A typical layered morphology is observed in the binary composites, where strong π-π interactions between the PEDOT-Tos polymer chains and a-SWCNT contribute to a highly conductive network. Besides, the acid-treatment acts as p-type doping for SWCNT, achieving a high electrical conductivity of 4731.6 ± 42.3 S cm for the PEDOT-Tos/a-SWCNT composite at the a-SWCNT content of 35 wt%. The corresponding power factor is calculated to be 119.4 ± 4.3 μW m K, around 108 times of that of the neat PEDOT-Tos. Moreover, a TE module with six PEDOT-Tos/a-SWCNT hybrid legs can generate an output power of 578.9 nW. The present study of the construction of layered conductive network, the employment of Tos as counterions for PEDOT and the acid-treatment for SWCNT promotes the design and fabrication of polymer-based composites for TE applications.