Abstract 3D covalent organic framework (3D COF) membranes with sub‐nanometer pore sizes and continuous channels offer a promising route for efficient molecular sieving. Nevertheless, fine‐tuning the pore sizes of dense COF membranes, especially those based on identical monomer compositions, presents a significant challenge. Herein, an effective and facile interfacial reaction strategy is developed to fabricate 3D COF 320 membranes with variable pore sizes. By simply changing composition of dual acids, both the framework structure and the membrane assembly process are regulated, enabling effective control over pore sizes and membrane thicknesses. The membranes exhibited high solvent permeance and could efficiently separate molecules with similar molecular weights. Moreover, further investigations revealed that the as‐prepared membranes are solvent‐responsive, enlarging their intrinsic pore sizes when exposed to methanol. By varying the ratio of water to methanol, the membrane could facilitate the graded molecular sieving of complex dye mixtures, achieving solute‐solute separation.