Proton exchange membranes (PEMs) have various applications, such as in electrolysis technology for hydrogen generation, vanadium flow batteries for energy storage, and fuel cells for energy conversion. To increase PEM performance and expand the range of PEM applications, the underlying transport mechanisms of PEMs need to be understood. Mesoporous silica thin films are versatile model materials for proton transport investigation and are prepared with a pore size of ≈12 nm and film thickness of ≈565 nm by evaporation‐induced self‐assembly, providing an ordered, mesoporous, rigid matrix that allows us to deduce the structure‐property relationship with respect to proton conductivity. Different amounts of sulfonic acid‐bearing groups are introduced into the mesopores using the grafting‐through polymerization of sulfopropylmethacrylate. The relationship between proton transport and the pH of the surrounding solution in poly‐sulfopropylmethacrylate‐functionalized mesopores is investigated using electrochemical impedance spectroscopy. The proton conductivity is found to depend on both the proton concentration in solution and the number of proton transporting groups inside the pore, indicating the major role of charge regulation and the confinement effect on proton transport.