Organic solvent nanofiltration (OSN) has become increasingly important in petrochemical and pharmaceutical industries, demanding superior and robust membranes. Herein, we report advanced OSN processes by designing three-dimensional covalent organic framework (3D COF) membranes through moderated interfacial crystallization. Nanoporous supports work as the moderator allowing the crystallization of 3D COF membranes. The 3D COF features sub-nanometer and anti-swelling channels, affording a sharp selectivity to fine targets with an exceptionally high and stable methanol permeance. Thus-synthesized membrane exhibits a record stability against high-concentration feeds and long-term operation for ≈1000 h. Moreover, we unambiguously demonstrate that our membrane holds excellent practicality in purifying active pharmaceutical ingredients from organic liquids. This work reveals the great potential of distinctive 3D COFs in producing prominent OSN membranes for industrial applications.