Thermoelectric (TE) generators, based on thermoelectric materials, can efficiently convert thermal energy into electricity via the Seebeck effect, showing great promise for wasteheat recovery research. Recent advancements in TE composites of conductive polymer/carbon nanotubes have been significant. This study evaluates the thermoelectric properties of organic TE films and generators by combining naphthalene diimide (NDI) polymers with single-walled carbon nanotubes (SWCNTs). The results reveal that P(NDI-HTO)/SWCNT composite films containing free radicals and alkyl side chains have enhanced thermoelectric properties compared to P(NDI-HT)/SWCNT composite films without free radicals and P(NDI-TP)/SWCNT composite films containing polar side chains. Among them, maximum power factors reach 264.1 ± 21.9 μW m −1 K −2 for p-type and 72.2 ± 1.5 μW m −1 K −2 for n-type composite films, marking increases of 113% and 32%, respectively, over pristine SWCNT films. Furthermore, a flexible thermoelectric generator based on P(NDI-HTO)/SWCNT, with five pairs of p−n junctions, achieves an output voltage of 28.8 mV and an output power of 1.2 μW at a 60 K temperature differential. These improvements in thermoelectric properties are primarily due to the effective modulation of molecular energy levels, enhancing the charge transfer process between NDI polymers and SWCNTs.