Hydrolytic stability and oxidative stability are the core properties of sulfonated polynaphthylimides (SPIs) as proton exchange membranes. The chemical structure of SPIs directly influences the performance. Herein, three different series of branched SPIs were designed and prepared using 1,3,5-tris (2-trifluoromethyl-4-aminophenoxy) benzene as a trifunctional monomer and three non-sulfonated diamine monomers, such as 4,4′-oxydianiline (ODA), 2,2-bis[4-(4-aminophenoxy)phenyl]hexafluoropropane (6FODA), and 4,4′-(9-fluorenylidene)dianiline (BFDA). The effect of the chemical structure and degree of branching on SPIs properties is discussed. The results showed that by controlling the chemical structure and degree of branching, the chemical stability of SPIs changed significantly. SPI-6FODA with two ether linkages and a hydrophobic CF3 group has higher hydrolytic stability than SPI-ODA with only one ether linkage. In addition, with the increase of the introduced B3 monomer, the oxidation stability of SPI-6FODA has been greatly improved. We successfully synthesized SPIs with a high hydrolytic stability and oxidative stability.