A new diamine monomer having alkyne side‐groups (DADAF) has been successfully synthesized, and it was used to prepare a series of sulfonated co‐polyimides (DFN‐XX) when reacted with 1,4,5,8‐naphthalenetetracarboxylic dianhydride along with different mole% of 4,4′‐diaminostilbene‐2,2′‐disulfonic acid. The membrane was made from the copolymers by solution casting route, and one of the copolymers DFN‐70 was used to prepare crosslinked membranes by adding a different amount of 1,6‐hexanediazide during solution casting step. The morphological transformation from non‐crosslinked S‐coPI to crosslinked S‐coPI was observed by employing transmission electron microscopy, atomic force microscopy, and small‐angle X‐ray scattering analyses. Compared to the non‐crosslinked DFN‐XX membranes, crosslinked DFN‐70 copolymer membranes showed low water uptake and improved mechanical and peroxide radical stability. Also, crosslinked DFN‐70 copolymer membranes showed significantly higher proton conductivities (0.004‐0.06 S cm−1) compared to those of DFN‐70 (0.003‐0.05 S cm−1) particularly, at 80°C when the relative humidity increased from 40% to 98%. Furthermore, crosslinked DFN‐70 copolymer membranes exhibited significantly enhanced performance in a microbial fuel cell (MFC) as compared to those of non‐crosslinked DFN‐70 membrane.