This work reports the preparation and characterization of mixed matrix membranes (MMMs) based on mesoporous ordered COK‐12 silica modified with 3‐aminopropyltrimethoxysilane as filler, and a series of polybenzimidazoles with different main‐chain structure as polymer matrix. Polybenzimidazoles (PBIs) were prepared from 3,3′‐diaminobenzidine and several dicarboxylic acids with different chemical structure. The physicochemical studies, as well as thermal, structural, and morphological properties of MMMs were determined by Fourier transform infrared spectroscopy, thermogravimetric analysis, X‐ray diffraction (XRD), and scanning electron microscopy. In addition, gas permeability properties of MMMs were tested by using a gas mixture of CO2/CH4 at different upstream pressures. Results indicated that thermal stability of PBI above 400°C is kept even after the addition of the modified COK‐12 silica. The d‐spacing of the PBI membranes determined by XRD was slightly increased with the addition of the modified COK‐12 silica particles. The permeability tests carried out at operating pressures of 50 and 150 psi showed that the addition of amino‐modified COK‐12 silica particles improved significantly the CO2 permeability of MMMs with respect to the pristine PBI. At the same time, the selectivity values were also enhanced, which in some cases were found to be more than double compared to the respective pristine membrane. The contribution of the modified COK‐12 silica on the gas transport properties was more promising in MMMs comprising PBIs with less rigid backbone chemical structure.