Covalent organic frameworks (COFs), with their regularly organized structures and solvent resistance, offer distinct advantages for constructing liquid-phase separation membranes. In nearly a decade of development, research has mainly focused on two-dimensional (2D) COFs, which yet give insufficient molecular selectivity due to inherent large pores. Here, we present a mixed-dimensional strategy of growing three-dimensional (3D) COFs on 2D COFs to build bilayered membranes for efficient organic solvent nanofiltration (OSN). The pores of 3D COFs interlace with those of 2D counterparts, resulting in a subnanoporous composite. We develop this 3D-/2D-COFs composite as robust membranes with a nanoscale thickness. The optimal bilayered membrane yields ethanol permeance of 12.2 L m−2 h−1 bar−1 with a molecular weight cutoff as low as ∼400 g mol−1, surpassing conventional COF-based OSN membranes. Importantly, the designed 3D-/2D-COFs membrane exhibits stable separation performance and excellent sieving ability to discriminate molecular mixtures. This exceptional molecular selectivity ultimately allows the separation of bioactive pharmaceuticals from impurities through our membrane. Overall, this work provides a design strategy for producing mixed-dimensional COF membranes to advance molecular separation in liquids.