An accurate prediction of ion selective adsorption in ion exchange membranes is essential to reflect the role of fixed charges on ion transport through the membrane in vanadium redox flow batteries (VRFB). Unlike those empirical models reported in the literature, this work reports on a new ion selective adsorption model with the Donnan effect considered for movable ions distributed in the membrane pores only. This model, no longer relying on empirical coefficients, is then applied to the calculation of ion transport through membranes in VRFBs. The model shows a more accurate prediction of vanadium crossover and membrane conductivity, and enables to capture the effect of key membrane properties on battery performance. It is found that (i) an increase in H2SO4 concentration reduces the electrolyte imbalance and improves the coulombic efficiency; (ii) an increase in membrane porosity significantly improves the membrane effective conductivity; (iii) the change of fixed charges should be careful to balance all performances. Therefore, membrane properties and operating conditions need proper adjustment to improve the battery performance, and our VRFB model is a good tool to help membrane optimization.