Conjugated microporous polymers (CMPs) are a novel class of microporous materials highly regarded as exceptional building blocks for the fabrication of high-performance organic solvent nanofiltration membranes. However, preparing CMP thin films remains a challenge, primarily due to the formation of insoluble powders via traditional solvothermal synthesis. Here, we introduce the innovative oxidative molecular layer deposition (oMLD) method for the fabrication of robust CMP membranes utilizing 3,3′-bithiophene (33DT) monomers. The oMLD method enables the direct fabrication of CMP thin films on substrates of varying shapes and allows precise control over membrane structure and separation performance by simply altering the deposition cycles. Benefiting from the abundant micropores and highly crosslinked structure, the resulting CMP membranes facilitate rapid solvent transport and present size-dependent solute−solute separations. In applications involving high-value separations, the P33DT membrane proves effective for pharmaceutical separation in organic solvents. To the best of our knowledge, this work represents the pioneering instance of fabricating CMP membranes via oMLD, significantly broadening the available preparation methods and potential separation applications for CMP membranes.