The design and synthesis of proton exchange membranes (PEMs) with controllable microstructure and sulfonation degree play a crucial role in enhancing their performance and expanding their application. In this study, the disulfonic acid monomer is designed and prepared to synthesize the comb‐like disulfonic PEMs with controllable ion exchange capacity. The results show that the side chain structure and more concentrated sulfonic acid groups facilitate the aggregation of sulfonic acid groups in the polymer, improve the microphase separation morphology of PEMs, and increase the ionic conductivity. The proton conductivity of the DS‐PXIDI‐60 membrane is approximately 300 mS cm−1. The PEMs with controllable microstructure are prepared by introducing comonomers, including 9,9‐dimethylxanthrene, biphenyl, and p‐terphenyl, with different reactivity, spatial structure, and solubility. Biphenyl is copolymerized to form a copolymer with an alternating structure, and 9, 9‐dimethylxanthrene is copolymerized to form a random copolymer. In addition, it is worth noting that p‐terphenyl is copolymerized to form a microblock structure of the copolymer, with more excellent comprehensive properties. DS‐PXITp‐60 exhibits better performance than Nafion 212 in redoxflow batteries and fuel cells. Therefore, such molecular design and synthesis strategies provide a reference guide for the development of high‐performance PEMs.