Abstract: The preparation of non-fluorinated proton exchange membranes (PEMs) includes post-sulfonation and direct polycondensation methods. The latter method involves the synthesis of sulfonated monomers, but the purification of sulfonated monomers is generally time-consuming. Herein, poly(arylene ether phosphine oxide)s (PAEPO) with pendant fluorenyl groups are synthesized by polycondensation of 9,9-bis(4-hydroxyphenyl) fluorene and bis(4-fluorophenyl) phenyl phosphine oxide, then the side-chain type sulfonated poly(arylene ether phosphine oxide)s (sPAEPO) are prepared by post-sulfonation as proton exchange membranes. NMR and FT-IR are used to determine the chemical structure of PAEPO and sPAEPO, and AFM is employed to characterize the microstructure of the sPAEPO PEMs. The dimensional stability and proton conductivity of the sPAEPO PEMs are also investigated. The results illustrate that the sulfonic acid groups in the side benzene rings facilitate the resultant membranes to form the microphase separation structures with well-connected hydrophilic phases, achieving high proton conductivity, low swelling, and excellent overall properties. At 80 °C, the as-made PEMs exhibit a swelling of 30%, less than that of most non-fluorinated PEMs, whereas their proton conductivity is 0.075 S/cm, close to that of Nafion 117. Besides, they also display excellent thermal stability and oxidation resistance. Therefore, the as-made PEMs show promising application prospects.