The trade-off between high proton conductivity and low vanadium ion permeability needs to be overcome urgently for membrane in vanadium redox flow battery (VRFB). A series of fluorine-containing branched sulfonated polyimide membranes with ionic cross-linking (c-FbSPI) and different degrees of sulfonation (40–70%) are prepared through polycondensation by introducing –CF3 group, branched structure and ionic cross-linking. The c-FbSPI membranes have much lower vanadium ion permeabilities (0.36–3.87 ✕ 10−7 cm2 min−1) and higher proton selectivities (0.89–4.20 ✕ 105 S min cm−3) comparing with Nafion 115 membrane, respectively. Besides, c-FbSPI membranes have outstanding chemical stabilities when immersing in strong acidic and oxidizing solution for 38 days. The VRFB with selected c-FbSPI-60 membrane shows lower self-discharge speed and higher charge-discharge capacity and energy comparing to those with Nafion 115 membrane. During 300-time cyclical charge-discharge measurement, the VRFB assembled with c-FbSPI-60 membrane shows higher coulombic efficiency (97–99.5%), energy efficiency (68.2–75.1%) and capacity retention (50.5–55.1%) compared with the VRFB using Nafion 115 membrane at 80–60 mA cm−2. This work provides a new approach for preparing high cost-performance aromatic polymer membrane, which is significant for accelerating the industrialization process of VRFB.