A sulfonated dicarboxylic monomer containing hexafluoroisopropyl, i.e., 3,3′-disulfonate-2,2-bis(4-carboxyphenyl)hexafluoropropane (SCFA), was prepared via sulfonation and oxidation to synthesize novel sulfonated polybenzothiazoles (sPBT-F) through polycondensation of 2,2-bis(4-carboxyphenyl)hexafluoropropane (CFA), SCFA, and 2,5-diamino-1,4-benzenedithiol dihydrochloride (DABDT). These sPBT-F series polymers exhibited excellent solubility due to the incorporation of a flexible hexafluoroisopropyl group. Meanwhile, the sPBT-F series polymers displayed high thermal stability and were used to prepare tough and soft membranes by solution casting. Interestingly, sPBT-F series membranes exhibited excellent water uptake and low swelling ratio, indicating excellent dimensional stability. AFM images displayed a region of obvious separation of light/dark phases, indicating high proton conductivity of sPBT-F series membranes. The sPBT-F82.5 membrane with a high degree of sulfonation demonstrated a conductivity of 0.14 S cm −1 at 80 °C and 100% RH, superior to the results of Nafion 117. Furthermore, the sPBT-F82.5 membrane displayed a maximum power density of 344.33 mW cm −2 and superb durability at a current density of 0.2 A cm −2 for 20 h. In summary, the sPBT-F polymers are potential matrix materials for PEMs.