Herein,we report the chemical in situ synthesis ofNafion/polyanilinecompositemembranes, including the different intrinsic oxidation states of polyaniline (PANI)such as leucoemeraldine base (LEB), emeraldine salt (ES), and pernigraniline base (PB). To better understand the role of the oxidation states of PANI, the microstructure changes of the composite membraneswere extensively characterized by using the Fourier transform infrared (FT-IR)ATR, scanning electron microscopy (SEM), atomic force microscopy (AFM), small-angle X-ray scattering (SAXS), and wide-angle X-ray diffraction (WAXD). From an applicative point of view, direct methanol fuel cell (DMFC)proton conductivities and methanol permeabilities aswell as the DMFC performances of the composite membranes were evaluated by AC impedance spectroscopy, permeability experiments, and single cell experiments. In particular, Naf-ES membranes exhibited a higher selectivity and superior cell performances compared to those of other oxidation states as a result of the effective modification of morphology and physicochemical properties of Nafion. The morphology and physicochemical properties of composite membranes were controlled by specifically manipulating the interactions between Nafion and PANIs by means of the oxidation states of PANI. These findings provide a deeper understanding of the influence of the PANI oxidation states on the composite materials as well as a practical strategy to enhance the physical properties and performances of pristine Nafion.