Nature possesses inexhaustible resources that inspire researchers to convert natural products into functional materials. Membranes with excellent permeability to balance the trade-off relationship between permeance and retention are highly desirable in the water-purification field. Herein, β-cyclodextrin (β-CD) and sodium ligninsulfonate (SLS) as derivatives of natural products were utilized to construct membranes with enhanced permeability via a facile molecularly engineered interfacial polymerization with 1,3,5-trimesoyl chloride. β-CD with an inner cavity of intrinsic 3D hollow bowls of several angstroms in diameter and hydrophilicity, it was utilized to reduce the permeation resistance of water. SLS endowed the newly designed SLS-CD-2 membrane with a highly negatively charged surface. Thus, the fabricated SLS-CD-2 membrane demonstrated a high permeance of 33.7 L m −2 h −1 bar −1 and a rejection rate of 99.8% for the filtration of Congo red solution. A 91.5% increase in permeance and a negligible change in retention were observed for the SLS-CD-2 membrane compared with those of the membrane without β-CD. The SLS-CD-2 membrane also exhibited excellent separation performance for the filtration of mixed-dye solution, high separation stability, and outstanding anti-pollution capacity. The results indicated the importance of the newly designed membrane in separation processes. • Natural-product-derived membranes: from natural products to functional membranes. • SLS and β-CD as derivatives of natural products were utilized to prepare membranes. • SLS-CD membranes were fabricated via IP reaction for anionic dye removal. • SLS-CD membranes with improved permeability were constructed by introducing β-CD. • SLS-CD-2 membrane had excellent permeance, rejection, anti-fouling, and stability.