The energy-filtering effect has been widely employed to elucidate the enhanced thermoelectric properties of organic/inorganic hybrids. However, the traditional Mott criterion cannot identify the energy-filtering effect of organic/inorganic hybrids due to the limitations of the Hall effect measurement in determining their carrier concentration. In this work, a carrier concentration-independent strategy under the theoretical framework of the Kang–Snyder model is proposed and demonstrated using PANI/MWCNT composites. The result indicates that the energy-filtering effect is triggered on increasing the temperature to 220 K. The energy-filtering effect gives a symmetry-breaking characteristic to the density of states of the charge carriers and leads to a higher thermopower of PANI/MWCNT than that of each constituent. From a morphological perspective, a paracrystalline PANI layer with a thickness of 3 nm is spontaneously assembled on the MWCNT network and serves as a metallic percolation pathway for carriers, resulting in a 5.56-fold increase in conductivity. The cooperative 3D carrier transport mode, including the 1D metallic transport along the paracrystalline PANI and the 2D cross-interface energy-filtering transport, co-determines a 4-fold increase in the power factors of PANI/MWCNT at 300 K. This work provides a physical insight into the improvement of the thermoelectric performance of organic/inorganic hybrids via the energy-filtering effect.