Improving the microphase separation structure of membranes is considered an effective strategy to solve the trade-off problem, which can increase the conductivity and reduce the swelling. This article designs poly(aryl alkylene) AEMs with different aryl backbone chains (biphenyl, p-terphenyl and m-terphenyl), with the goal of examining the effect of spatial structure main chains on the membrane performance. It is found that the membrane (m-QTPNP) has a better microphase separation structure and a conductivity of 143.5 mS cm−1 (80 °C) via SAXS, TEM and AFM. Due to the lower IEC (2.23 meq g−1), m-QTPNP has a good anti-swelling performance. During tensile testing, the elongation at break of m-QTPNP can reach 105.5% (wet state). Moreover, due to the obvious microphase separation, the attack of OH− on the quaternized groups is reduced, and m-QTPNP has a conductivity retention rate of 95.5% (80 °C, 2 M NaOH, 1560 h). In addition, the peak power density (PPD) of the H2/O2 single cell equipped with m-QTPNP can reach 749 mW cm−2 (80 °C). After 90 h of durability testing, the voltage decayed to 92.2%, with a decay rate of 0.54 mV h−1.