The effect of the local structure of Co-doped amorphous silica on the hydrogen transport property was studied with the aim to improve the high-temperature hydrogen-permselectivity of microporous amorphous silica-based membranes. Co-Doped silica materials with measured Co/Si atomic ratios ranging from 0.01 to 0.18 were successfully synthesized through the polymer-derived ceramic (PDC) route. X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM) analyses confirmed the amorphous state of the polymer-derived Co-doped silica, while both X-ray photoelectron and Fourier transform infrared (FT-IR) spectroscopy analyses revealed that the divalent Co cation (Co 2+) modified the matrix amorphous silica network to form hydrogen-bonded silanol. After dehydration treatment at 500°C in argon, hydrogen (H)/deuterium (D) isotope exchange behavior on the surface silanol groups (Si-OH/OD conversion) of the polymer-derived non-doped and Co-doped amorphous silica was in situ monitored by measuring diffuse reflectance infrared Fourier transform (DRIFT) spectra at 500°C. The self-diffusion coefficient for OH/OD conversion of free silanol groups of non-doped silica was 6.1 × 10 −15 m 2 s −1 , while that on the hydrogen bonded Si-OH was found to reach 15.6 × 10 −15 m 2 s −1 by Co-doping at the measured Co/Si atomic ratio of 0.05.The effect of the amount of Co 2+ doping on the hydrogen transport property was further studied by scanning transmission electron microscopy and electron energy loss spectroscopy (STEM-EELS) analyses, and it was suggested that a rather small amount of Co-doping, i.e. Co/Si atomic ratio of 0.05 was effective for enhancing high-temperature hydrogen permeance through microporous amorphous silica-based membranes.