High proton selectivity is essential for the use of ion exchange membranes (IEMs) in vanadium redox flow battery (VRFB) systems. Herein, a series of poly (oxyphenylene benzimidazole) (OPBI)/ionic liquid (IL) composite membranes was prepared by mixing OPBI with 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm]BF4) to obtain membranes with high proton selectivity. Because ILs formed hydrogen bonds with the polymer chains, ILs were able to remain within the membranes themselves. Proton conductivity and vanadium permeability of the membranes were examined for membrane characterization. Surprisingly, because of the Donnan exclusion effect between the cations of the ILs and the vanadium ions, the trade-off effect of traditional IEM modification methods was overcome. Therefore, as the IL content increased, the vanadium resistance and proton conductivity of the composite membranes increased. The proton selectivity of optimized OPBI/BF4-20 composite membrane was 1.41 × 106 S min cm−3, which was much higher than that of the unmodified OPBI membrane (6.06 × 105 S min cm−3) or a commercialized Nafion 115 membrane (1.61 × 104 S min cm−3). More importantly, the OPBI/BF4-20 composite membrane exhibited higher coulombic efficiency (CE, 99.24%), voltage efficiency (VE, 93.10%) and energy efficiency (EE, 92.39%) at 40 mA cm−2 than the unmodified OPBI (CE 98.06%, VE 90.67% and EE 88.86%) and Nafion 115 membranes (CE 95.44%, VE 91.75% and EE 87.57%). Furthermore, the cell employing the OPBI/BF4-20 membrane exhibited no significant decrease in battery efficiency after a 1000-time cycles test. In conclusion, the research and application of IL-embedded composite membranes in a VRFB system could potentially change the limitations of traditional modification methods.