In this paper, a new type of ultrathin sulfonated mesoporous silica film (SMSF) with well-ordered perpendicular mesochannels was in-situ synthesized by Stöber approach and co-condensation method. The mesostructure of the synthesized SMSF was characterized. The results of small-angle XRD, high-resolution TEM, and cyclic voltammetry (CV) exhibited that, after loading of MPTMS, SMSF had an ordered mesostructure with a perpendicular orientation and open ends. SEM showed that SMSF could be entirely transferred and easily handled. FT-IR presented that sulfonic groups were successfully added to the surface of the nanochannels of silica film. Compared with mesoporous silica film (MSF) and commercial cation exchange membrane (CEM), SMSF had the highest permselectivity. The permselectivity of SMSF was not lined with the loading of the sulfonic groups (–SO3H). The highest permselectivity of SMSF to Na[Formula: see text] was 94% when the loading of MPTMS was 5.98% (wt.%). SMSF is a promising material in the application of salinity gradient energy harvest.