Ultrathin semi-interpenetrating proton exchange membranes (SIPN PEMs) comprised of conductive perfluorinated sulfonic acid resin (PFSA) and cross-linked polydivinylbenzene (PDVB) have been fabricated. The SIPN PEMs containing both conductive and cross-linked components exhibited better mechanical stability and electrochemical properties than recast PFSA. The SIPN-3 membrane with the lowest IEC 0.8493 mmol g−1 among the three SIPN PEM samples, however, showed the highest proton conductivity, 0.083 S cm−1, and a comparatively low swelling ratio of 10.12% at 80 °C in deionized water. At the same time, the unique structure and lower thickness endowed the membranes with outstanding fuel cell performance due to the decreased proton transfer resistance. The results show that SIPN-3 with 964.6 mW·cm−2 power density was obtained, and the gas crossover current density was only 1.34 mA·cm−2, which was lower than that for the recast PFSA (1.5 mA·cm−2) and Nafion® NC700 (2.75 mA·cm−2). Thus, constructing a semi-interpenetrating network is certified to enhance properties of the membrane prominently, which has the potential to be applied in PEMFC.