Cationic gas-permeable molds fabricated via sol–gel polymerization undergo cationic polymerization using epoxide, resulting in gas permeability owing to their cross-linked structures. By applying this cationic gas-permeable mold to nano-injection molding, which is used for the mass production of resins, nano-protrusion structures with a height of approximately 300 nm and a pitch of approximately 400 nm were produced. The molding defects caused by gas entrapment in the air and cavities when using conventional gas-impermeable metal molds were improved, and the cationic gas-permeable mold could be continuously fabricated for 3000 shots under non-vacuum conditions. The results of the mechanical evaluations showed improved thermal stability and Martens hardness, which is expected to lead to the advanced production of resin nano-structures. Furthermore, the surface roughness of the nano-protrusion structures fabricated using injection molding improved the water contact angle by approximately 46°, contributing to the development of various hydrophobic materials in the future.