Abstract For organic solar cells, the different surface‐free energies (SFE) of donors and acceptors leads to inhomogeneous distribution at the upper and bottom surfaces of the photoactive layer. Undesired distribution of donors and acceptors is unfavorable for charge collection. Adjusting the SFE of the underlying interfacial layer can effectively change the distribution of donors and acceptors within the photoactive layer. Herein, Nafion, a perfluorinated polymer containing the fluorocarbon backbone and perfluorovinyl ether branch with sulfonic acid end groups, is introduced to adjust the SFE of poly‐(3,4‐ethylenedioxythiophene):poly‐(styrenesulphonicacid) (PEDOT:PSS). The work‐function change of the PEDOT:PSS before and after doping with Nafion is explored by ultraviolet photoelectron spectroscopy. The contact angles of water and diiodomethane on the PEDOT:PSS and PEDOT:PSS‐Nafion are measured and their SFE are calculated from the Owens formula. Interfacial layer induced phase separation is investigated by energy‐dispersive spectroscopy and transmission electron microscopy. The device resistance and carrier lifetime are investigated by electrochemical impedance spectroscopy and intensity‐modulated photovoltage spectroscopy. By accurately adjusting the ratio of Nafion to PEDOT:PSS, the optimized device with PBDB‐TCL:IT‐4F achieves the power conversion efficiency (PCE) of 14.12% and the device based on PEDOT:PSS‐Nafion with PBDB‐TF:Y6 achieves the PCE of 16.31%.