Fluorocarbon-modified silica membranes were deposited on γ-Al2O3/α-Al2O3 supports by the sol−gel technique for hydrogen separation. The hydrophobic property, pore structure, gas transport and separation performance, and hydrothermal stability of the modified membranes were investigated. It is observed that the water contact angle increases from 27.2 ± 1.5° for the pure silica membranes to 115.0 ± 1.2° for the modified ones with a (trifluoropropyl)triethoxysilane (TFPTES)/tetraethyl orthosilicate (TEOS) molar ratio of 0.6. The modified membranes preserve a microporous structure with a micropore volume of 0.14 cm3/g and a pore size of 0.5 nm. A single gas permeation of H2 and CO2 through the modified membranes presents small positive apparent thermal activation energies, indicating a dominant microporous membrane transport. At 200 °C, a single H2 permeance of 3.1 × 10−6 mol m−2 s−1 Pa−1 and a H2/CO2 permselectivity of 15.2 were obtained after proper correction for the support resistance and the contribution from the defects. In the gas mixture measurement, the H2 permeance and the H2/CO2 separation factor almost remain constant at 200 °C with a water vapor pressure of 1.2 × 104 Pa for at least 220 h, indicating that the modified membranes are hydrothermally stable, benefiting from the integrity of the microporous structure due to the fluorocarbon modification.