Sulfonated poly(fluorenyl ether ketone) (SPFEK) membranes were modified with layered proton conductors zirconium phosphate sulfophenylenphosphonates (ZrPSPP) to improve the proton conductivity and mitigate vanadium ions crossover. The effects of ZrPSPP filler loading on the microstructure and chemical–physical property of SPFEK/ZrPSPP composite membranes as well as the vanadium redox flow battery performance are reported. The uniform dispersion of ZrPSPP sheets in the SPFEK matrix is investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive X-ray analysis (EDX). Since the sulfonic acid groups on the aromatic main-chains are less flexible, the proton channels in the pristine SPFEK membranes are relatively narrow and not well connected. The intensive sulfonic acid groups on ZrPSPP fillers increase the water uptake and the hydrophobic/hydrophilic microphase separation of the composite membranes, resulting in improved proton conductivity. The impermeable nanoplates demonstrate to be a potential physical barrier for vanadium ion diffusion. The VRB assembled with the SPFEK/5 wt%ZrPSPP composite membrane shows longest discharge time and maximal coulombic efficiency among VRBs using the pristine SPFEK and other hybrid SPFEK/ZrPSPP and Nafion 117 membranes.