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A key challenge in efficient molecular separation is fabricating large‐scale, highly selective polymeric membranes with precise pore control at the molecular scale. Herein, a new contorted monomer 6,6′‐dihydroxy‐2,2′‐biphenyldiamine (DHBIPDA) is introduced as a building block to generate cross‐linked, ultra‐thin microporous nanofilms (sub‐10 nm) via interfacial polymerization, enabling rapid, and precise molecular nanofiltration. Using diacyl chloride (TPC) as the cross‐linker instead of trimesoyl chloride (TMC) significantly reduces the pore sizes within the membranes and achieves a narrower pore distribution due to a semi‐crystalline structure. The film structures are confirmed using comprehensive characterization techniques including wide‐angle X‐ray scattering (WAXS), X‐ray diffraction (XRD), positron annihilation lifetime spectroscopy (PALS), CO2 adsorption analysis, and molecular‐scale simulation. The DHBIPDA/TPC and DHBIPDA/TMC membranes achieve methanol permeance values of up to 16.4 and 15.1 LMH bar−1 coupled with molecular weight cutoffs (MWCOs) as low as 283 and 306 Da, respectively. The DHBIPDA/TPC membrane demonstrates both higher permeance and higher selectivity compared to its relatively disordered counterpart DHBIPDA/TMC, consistent with characterization data. The DHBIPDA‐derived membrane efficiently separates dye mixtures with similar molecular weights and enables effective recycling of organometallic homogeneous catalysts, suggesting its potential for industrial applications. [ABSTRACT FROM AUTHOR]