A series of novel phenolphthalein-containing sulfonated poly(arylene ether phosphine oxide)s (sPAEPP) with various sulfonation degrees were synthesized by direct polycondensation. The structure of sPAEPP was confirmed by 1 H-NMR, 13 C-NMR, and IR spectroscopy. The high-molecular weight of these polymers was determined by gel permeation chromatography (GPC). The transparent, tough, and flexible membranes could be achieved by solution casting. The macroscopic properties and microstructure of the obtained membranes were investigated in detail. The results showed that these sPAEPP membranes displayed excellent properties in terms of swelling, proton conductivity, and methanol permeability. For example, sPAEPP-100 membrane exhibited an appropriate water uptake of 33.1%, a swelling ratio of only 11.7% (lower than 20.1% of Nafion 117), a proton conductivity of 0.11 S cm −1 (similar to that of Nafion 117) at 80 C, and a methanol permeability of 4.82 × 10 −7 cm 2 s −1 . Meanwhile, it also presented outstanding oxidative stability. Atomic force microscope (AFM) micrographs showed that the hydrophilic domains of the sPAEPP-100 membrane formed connected and narrow ionic channels, which contributed to its high proton conductivity and good dimensional stability. As a result, sPAEPP-100 membrane displays excellent application prospect for fuel cells.