Membrane separation technologies are of great interest in industrial processes such as water purification, gas separation, and materials synthesis. However, commercial filtration membranes have broad pore size distributions, leading to poor size cutoff properties. In this work, mesoporous silica thin membranes with uniform and large vertical mesochannels are synthesized via a simple biphase stratification growth method, which possess an intact structure over centimeter size, ultrathin thickness (≤50 nm), high surface areas (up to 1420 m2 g−1), and tunable pore sizes from ≈2.8 to 11.8 nm by adjusting the micelle parameters. The nanofilter devices based on the free-standing mesoporous silica thin membranes show excellent performances in separating differently sized gold nanoparticles (>91.8%) and proteins (>93.1%) due to the uniform pore channels. This work paves a promising way to develop new membranes with well-defined pore diameters for highly efficient nanosize-based separation at the macroscale.