In this work, we report a new class of organic–inorganic nanocomposite ion-exchange membranes containing a sulfonated functionalized polymer (sulfonated polyethersulfone) and sulfonated mesoporous silica (SS). The effect of SS filler size (20 and 100 nm) on membrane structures and properties has been investigated. The results revealed the significant impact of filler sizes on macroscopic properties, such as morphologies, physico-electrochemical performance, and mechanical and thermal stabilities of the resultant composite membranes. The appropriate amount of smaller-sized SS fillers (20 nm diameter) led to better overall properties of the composite membranes with a conductivity up to 2.7 mS cm–1, a permselectivity of 98% (around 640% and 16% improvement of conductivity and permselectivity compared with the pristine membranes, respectively), and high thermal and mechanical stability due to intimate polymer–inorganic filler interaction. The performance of the composite membranes in the desalination of a NaCl solution was evaluated by a lab-scale electrodialysis cell in comparison with a benchmark membrane, FKE. The results revealed that the optimized composite with 0.5 wt % inorganic SS additive with a smaller particle size (20 nm diameter) exhibited an overall desalination performance comparable to that of FKE. Moreover, the energy consumption of the composite membrane was brought down to nearly a half compared to that of the pristine polymer membrane.