A novel epoxy-based semi-interpenetrating polymer networks membrane (SPIX-EP40) as the proton exchange membrane was prepared by a flexible epoxy network with sulfonated polyimide. A series of sulfonated polyamic acid (SPAA) were prepared from 1,4,5,8-naphthalenetetracarboxylic dianhydride, 2,2-benzidinedisulfonic acid (BDSA) and nonsulfonated diamines, such as 4,4′-diaminodiphenyl sulfone. Solid-state C13 nuclear magnetic resonance spectra and Fourier transform infrared spectroscopy were used to verify the synchronization of the imidization of SPAA and the crosslinking reactions of epoxy. The sulfonationity of the copolymers was regulated through a variation in the molar ratio of BDSA to diamine. These membranes owned a good thermal stability and exhibited high proton conductivity that was measured as a function of temperature. The resulting SPI0.7-EP40 and SPI0.8-EP40, at 100% relative humidity, displayed proton conductivities higher than those of Nafion® 117. The membranes displayed higher conductivities than Nafion® membranes because of owning higher activational energies and higher ion exchange capacities. An isotropic swelling phenomenon in water was found for the membrane. From the results of water uptake and the microstructure analyses using transmission electron microscopy (TEM) on different sulfonated levels, it was found that the number of water clusters in SPIX-EP40 membranes increased as the increasing water uptake and the size of water cluster were changed with the sulfonation levels. TEM confirmed the widespread and well-connected hydrophilic domains, demonstrating the presence of the favorable proton-transporting performances of the SPIX-EP40 membrane.