An ideal molecular filtration membranes should be highly permeable and selective, thus desiring the membranes to be ultrathin, be highly porous, and consists of small and uniform pores or channels. In this work, we report the molecular filtration by free-standing ultrathin silica nanochannel membranes (SNMs) using a U-shaped cell and spectrophotometric detection, focusing on the quantitative evaluation of permeability and selectivity of SNMs. Thanks to the ultrasmall channel size, namely, ∼2-3 nm, and the negatively charged channel surface arising from the deprotonation of silanol groups, the SNM displayed excellent size and charge selectivity for molecular filtration. The selectivity coefficient for separation of small methyl viologen from large cytochrome c is as high as 273, because of the uniform pore/channel size. The charge-based filtration can be modulated by the salt concentration and solution pH, which control the overlap of radial electrical double layer and surface charge sign/density, respectively. Owing to the high relative pore density, namely, 16.7%, and the straight and vertical channel orientation, the SNM is highly permeable, displaying a molecule flux much higher than commercially available dialysis membrane and others reported previously. In addition, we demonstrated that, by biasing a small voltage across the SNM, both the flux and separation selectivity could be significantly enhanced.