Nanofiltration (NF) membranes with in situ assembled silica on the surface and in the pores were proposed and successfully prepared for vanadium redox flow battery (VRB) applications to improve the vanadium/proton selectivity. VRBs assembled with the modified membranes exhibited much higher Coulombic efficiency than that with original NF membranes, while with a similar voltage efficiency. The results indicate that silica modification can effectively increase the membranes' ion selectivity and maintain good ion-conducting properties. The concept provides an effective way to fabricate high performance porous membranes for VRB applications.