The creation of uniformly molecular-sized through-pores within polymeric membranes and the direct evidence of these pores are essential for fundamentally understanding the transport mechanism and improving separation efficiency. Herein, we report an electric-field-assisted interface synthesis approach to fabricating large-area covalent organic framework (COF) membranes that consist of preferentially oriented single-crystalline COF domains. These single-crystalline frameworks were translated into high-density, vertically aligned through-pores across the entire membrane, enabling the direct visualization of membrane pores with an ultrahigh resolution of 2 Å using the low-dose high-resolution transmission electron microscopy technique (HRTEM). The density of directly visualized through-pores was quantified to be 1.2 × 1017 m-2, approaching theoretical predictions. These COF membranes demonstrate ultrahigh solvent permeability, which is 10 times higher than that of state-of-the-art organic solvent nanofiltration membranes. When applied to high-value pharmaceutical separations, their COF membranes exhibit 2 orders of magnitude higher methanol permeance and 20-fold greater enrichment efficiency than their commercial counterparts.