Fluorinated C60 (F-C60) is a p-type organic semiconductor with a deep highest occupied molecular orbital (HOMO) level and it was used to modulate the band structure of reduced graphene oxide (rGO). The HOMO level of rGO has been tailored by adjusting the ratio between rGO and F-C60. As-prepared rGO/F-C60 hybrids were subsequently integrated to the conductive polymer, poly (3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS), at a very low fraction (below the percolation threshold). The interfaces between rGO/F-C60 nanohybrids and polymer host served as Schottky barriers to selectively scatter low-energy carriers dependent on the interfacial barriers. The highest power factor reaches 83.2 μW/m K2 at an interfacial barrier of 0.7 eV for a 2.5 wt% loading fraction, indicating 19-fold enhancement in comparison to the conductive PEDOT:PSS with a power factor of 4.38 μW/m K2. More interestingly, F-C60 nanoparticles on rGO surfaces hinder thermal transport by effective phonon scattering, resulting in a figure of merit (ZT) of 0.10. In contrast, incorporation of inorganic nanoparticles may compromise thermoelectric properties for a low ZT due to the increase of thermal conductivity.