In our previous work, Nafion/SiO2 hybrid membrane was prepared via in situ sol–gel method and used for the vanadium redox flow battery (VRB) system. The VRB with modified Nafion membrane has shown great advantages over that of the VRB with Nafion membrane. In this work, a novel Nafion/organically modified silicate (ORMOSIL) hybrids membrane was prepared via in situ sol–gel reactions for mixtures of tetraethoxysilane (TEOS) and diethoxydimethylsilane (DEDMS). The primary properties of Nafion/ORMOSIL hybrids membrane were measured and compared with Nafion and Nafion/SiO2 hybrid membrane. The permeability of vanadium ions through the Nafion/ORMOSIL hybrids membrane was measured using an UV–vis spectrophotometer. The results indicate that the hybrids membrane has a dramatic reduction in crossover of vanadium ions compared with Nafion membrane. Fourier transform infrared spectra (FT-IR) analysis of the hybrids membrane reveals that the ORMOSIL phase is well formed within hybrids membrane. Cell tests identify that the VRB with Nafion/ORMOSIL hybrids membrane presents a higher coulombic efficiency (CE) and energy efficiency (EE) compared with that of the VRB with Nafion and Nafion/SiO2 hybrid membrane. The highest EE of the VRB with Nafion/ORMOSIL hybrids membrane is 87.4% at 20mAcm−2, while the EE of VRB with Nafion and the EE of VRB with Nafion/SiO2 hybrid membrane are only 73.8% and 79.9% at the same current density. The CE and EE of VRB with Nafion/ORMOSIL hybrids membrane is nearly no decay after cycling more than 100 times (60mAcm−2), which proves the Nafion/ORMOSIL hybrids membrane possesses high chemical stability during long charge–discharge process under strong acid solutions. The self-discharge rate of the VRB with Nafion/ORMOSIL hybrids membrane is the slowest among the VRB with Nafion, Nafion/SiO2 and Nafion/ORMOSIL membrane, which further proves the excellent vanadium ions blocking characteristic of the prepared hybrids membrane.