A novel proton conductive nanofiber composite membrane, which was composed of sulfonated polyimide (SPI) nanofibers and a typical polymer electrolyte, Nafion, was developed to improve electrolyte characteristics, especially proton conductivity at low relative humidity, for polymer electrolyte fuel cells. In addition to the contribution of the SPI nanofibers that were revealed to possess ultra-high proton conductivities in our previous study, the Nafion matrix indicated unique morphology in the composite membrane. The TEM observation suggested that the sulfonic acid groups in the Nafion matrix were attracted to the SPI nanofibers during the membrane formation process,to construct acid-condensed layer near the nanofibers. Such acid-condensed layer at the interface of SPI nanofibers and Nafion matrix should have a positive impact on the proton conduction and water diffusion, especially under the low relative humidity conditions. Improved gas barrier property and membrane stability were also achieved by using the proton conductive SPI nanofibers as a framework for the polymer electrolyte membrane.