Covalent organic framework (COF) exhibits the great potential to promote proton conduction under low relative humidity for proton exchange membranes (PEMs). In this research, quick and stable proton conduction has been achieved since the prepared COF and polyvinylidene fluoride (PVDF) nanofibers are believed to constitute successive proton conduction channels. The PVDF-COF nanofibers membrane is prepared through the in-situ growth of COF along PVDF nanofibers. The fine compatibility can drive the stable combination of COF with the PVDF nanofibers in PVDF-COF nanofibers. Most importantly, the fibrous PVDF nanofibers accelerate proton conduction through confining the proton conduction pathways. Additionally, ionic liquids of 1-butyl-3-methylimidazolium chloride (BmimCl) and 1-butyl-3-methylimidazole hexafluorophosphate (BmimPF6) as proton conduction carriers have been introduced to accelerate proton conduction in the prepared PVDF-COF/BmimCl/PA and PVDF-COF/BmimPF6/PA membranes. Phosphoric acid (PA) molecules are combined by COF and ionic liquid cations with the formation of intermolecular hydrogen bonds. As a result, the PVDF-COF/BmimPF6/PA membrane exhibits the proton conductivity of (1.81 ± 0.07) × 10−1 S/cm at 160 °C. The long-term proton conductivity stability is determined, deriving from the proton conductivities of 1.77×10−2 S/cm at 80 °C and 1.42×10−2 S/cm at 110 °C in the 400 h non-stop measurement. The single fuel cell equipped with the PVDF-COF/BmimPF6/PA membrane represents the open circuit voltage of 0.927 V and the peak power density of 178.8 mW/cm2 at 100 °C, 0.907 V and 326.5 mW/cm2 at 120 °C.