PEDOT-PSS is a widely used hole extraction layer in polymer solar cells (PSCs). However, its acidic and hygroscopic nature usually affects the long-term stability of the photovoltaic devices. Herein, we report an effective method to enhance the conductivity and stability of PEDOT-PSS film by doping with an amphiphilic perfluorosulfonic copolymer, Nafion. The highly hydrophobic fluorocarbon backbone of Nafion preferentially interacts with the hydrophobic PEDOT of PEDOT-PSS, while the highly hydrophilic -SO3H groups preferentially interact with hydrophilic PSS chains, inducing the PEDOT chains separated from the PSS chains by Nafion. The conductivity and the surface morphology of the Nafion-doped PEDOT-PSS layer were investigated by four-point probe and atomic force microscope, respectively. The optical properties of the Nafion doped PEDOT-PSS film and the photoactive layer spin-coated on it were studied by transmittance and reflection spectra. With Nafion doped PEDOT-PSS hole extraction layer (HEL), the power conversion efficiency of the PSCs based on poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) reaches 4.63%, increased by 14.3% in comparison with that of the control devices. Furthermore, the lifetime of the devices with Nafion doped PEDOT-PSS HEL is greatly enhanced.