This study focused on the impact of virgin polymer structure and microstructure on the transport properties of irradiated polyimide. Two fluorine containing polyimide isomers (6FDA-6FpDA and 6FDA-6FmDA) that differ solely in the location of the linkage between the diamine and dianhydride residues were used for this study. While these polymers differ in the location of a single bond, the virgin transport properties are dramatically different. The para connected isomer (6FDA-6FpDA) has much higher permeabilities and lower selectivities than the meta connect isomer (6FDA-6FmDA). The pure gas permeabilities in polyimide-ceramic composite membranes following H+ ion irradiation over a wide range of doses will be compared for these polyimide isomers. In addition, the evolution in chemical structure was monitored using Fourier transform infrared spectroscopy (FTIR). These polymers exhibited different decay rate in chemical structure following ion irradiation. Interestingly, the evolution in gas transport properties of these polymers following H+ ion irradiation was also quite different. We will discuss how the microstructure would affect the gas permeation properties of ion beam modification of polymer.