Polyaniline (PANI) is one of the most promising candidates for flexible organic thermoelectric (TE) applications owing to its relatively low cost and high stability. Herein, the self-assembled supramolecule (SAS) (3,6-dioctyldecyloxy-1,4-benzenedicarboxylic acid) was used as an additive and was introduced into PANI films as a template. Raman spectroscopy, X-ray diffraction, and conductive atomic force microscopy analyses demonstrated that the highly ordered chain structure of PANI was achieved by chemical interactions between PANI and the SAS. Moreover, the ordered regions in the PANI-SAS film increased with a decrease in the film thickness. Consequently, the TE properties of PANI-SAS films were not only much higher than those of PANI films, but they also increased with a decrease in film thickness. The maximum TE power factor of the PANI-SAS film reached 31Wm(-1)K(-2), which is approximately six times higher than the power factor of a PANI film with a similar thickness. This work offers a promising way to prepare PANI thin films with enhanced TE properties.