In this work, the polymerization of hydrophobic pentafluorophenylethyl into the high conductivity poly (acenaphthenyl aryl piperidinium) backbone was catalyzed by an efficient and facile one-pot method with super-strong acids to build enhanced phase separation structures while maintaining low swelling. The prepared QPANTP-20-F15 membrane exhibited the most significant hydrophilic-hydrophobic separation phenomenon, with the conductivity as high as 192.19 mS cm−1 at 80 °C. Due to the incorporation of hydrophobic fluorinated groups, the water uptake of the membrane was limited, and its mechanical (71.0 MPa under hydrated condition) and dimensional stability property (11.32% swelling) showed improved results. In addition, after 1200 h at 80 °C in 3 M/5 M NaOH solution, the structure of the prepared polymer exhibited excellent chemical stability property, with conductivity remaining of 95.04% and 86.38%, respectively. With current density of 706 mA cm−2 at 80 °C, the AEMFCs achieved a peak power density of 321 mW cm−2.