Organic thermoelectric (TE) materials are very attractive due to easy processing, material abundance, and environmentally-benign characteristics, but their potential is significantly restricted by the inferior thermoelectric properties. In this work, noncovalently functionalized graphene with fullerene by π-π stacking in a liquid-liquid interface was integrated into poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate). Graphene helps to improve electrical conductivity while fullerene enhances the Seebeck coefficient and hinders thermal conductivity, resulting in the synergistic effect on enhancing thermoelectric properties. With the integration of nanohybrids, the electrical conductivity increased from ~10000 to ~70000 S/m, the thermal conductivity changed from 0.2 to 2 W·K−1m−1 while the Seebeck coefficient was enhanced by around 4-fold. As a result, nanohybrids-based polymer composites demonstrated the figure of merit (ZT) as high as 6.7 × 10−2, indicating an enhancement of more than one order of magnitude in comparison to single-phase filler-based polymer composites with ZT at the level of 10−3.