In this work, the thermoelectric performance of poly(3-hexylthiophene)/single walled carbon nanotubes (P3HT/SWCNTs) composite films has been effectively improved by HClO4 post-treatment. The P3HT/SWCNTs composite films with 20 wt% of fillers achieved an optimal power factor of 27.99 μW m−1 K−2 after HClO4 post-treatment for 2 h. The increased thermoelectric performance of P3HT/SWCNTs composite films can be attributed to the HClO4 treatment that can promote the transitions of the P3HT spacers between the adjacent SWCNTs from their neutral state to the bipolaron state, which significantly increased the electrical conductivity of the composite films. P3HT/SWCNTs composite films filled with low-content SWCNTs possessed excellent flexibility. This excellent performance of P3HT/SWCNTs composite films should be attributed to the combination of advantages of organic/inorganic hybridization and acid post-treatment. This is an important strategy to improve the performance of thermoelectric materials in recent years.