A series of novel organic–inorganic hybrid membranes with special microstructure, based on sulfonated poly (fluorenyl ether ketone) ionomer (SFPEK, IEC=1.92mequiv.g−1) and SiO2 or sulfonic acid group containing SiO2 (SiO2–SO3H), has been successfully designed and prepared for vanadium redox flow battery (VRB) application. The SiO2–SO3H is synthesized by co-condensation of tetraethoxysilane and γ-propyl mercaptotrimethoxysilane via sol–gel process to control the same IEC with neat SPFEK. The hybrid membranes are prepared by simply adding the inorganic particles into the SPFEK solution in N,N′-dimethylacetamide, followed by ultrasonic dispersion, casting and profiled temperature drying process. The morphology is examined by SEM-EDX which is applied to the top surface, bottom surface and cross-section of the hybrid membranes. The water uptake, oxidative stability, thermal property, mechanical property, proton conductivity, VO2+ permeability and single cell performance are investigated in detail in order to understand the relationship between morphology and property of the membranes. All the hybrid membranes show dramatically improved proton selectivity at 20°C and 40°C when compared with Nafion117. The VRB assembled with the SPFEK/3%SiO2 and SPFEK/9%SiO2 membranes exhibit higher coulombic efficiency and average discharge voltage than the VRB assembled with the SPFEK membrane at all the tested current densities.