Polymer blending is a facile method for preparing cost-effective membranes for redox flow batteries with improved properties. It is of great importance to reveal the effects of the polymer chain morphology on the membrane properties and to successfully tailor the performance. Phase separations of various Nafion-based polymer blends are predicted and membranes with well-controlled phase separation are obtained. It is indicated that the domain size of the polymer phase separation significantly influences the ion transport behavior and thus, the battery performance of the redox flow battery. By varying the polymer compatibility, the Nafion/PVDF-HFP blend membrane possesses the highest proton conductivity among the different blend membranes due to the minimized domain of phase separation. Its proton conductivity reaches 53.61 mS/cm, almost 3 folds of that of the Nafion/PVDF membrane with the same Nafion content of 60 wt%. The cell equipped with the Nafion/PVDF-HFP blend membrane (50 wt% Nafion) shows a voltage efficiency of 87.45% and an energy efficiency of 83.83% at 100 mA/cm2, which are comparable to the pure Nafion membrane. The blend membrane shows excellent chemical stability during an 800-cycle charge-discharge test. By fine-tuning polymer phase separation, cost-effective blend membranes with significantly enhanced performance for redox flow batteries can be obtained.