In the context of sustainable development, chirality, especially chiral drugs, has attracted great interest in the pharmaceutical industry, yet the smart and sensitive separation of enantiomers still presents a major scientific challenge. Herein, inspired by supramolecular templating via chiral transcription nanoparticles, an artificial chiral nanochannel membrane with asymmetric structure, porosity, and abundant chiral surface is fabricated for smart and sensitive enantiomer recognition and separation. Constructed from chiral transcript mesoporous silica (CMS) super-assembled on a porous anode alumina oxide (AAO) support, the obtained heterostructured chiral membrane (CMS/AAO) exhibits enhanced enantioseparation (approximately 170% compared to the supramolecular-templated nanoparticles) among a series of amino acids with various isoelectric points (PIs). Especially for amino acids with a PI greater than 7, the couple-accelerated enantioseparation (CAE) can be achieved for the first time. Further analysis using an osmotic energy conversion test and simulations based on the Poisson–Nernst–Planck (PNP) equations confirm that the heterostructure and charge polarity are the key to achieve chiral amino acids and ion separation. We expect this work will inspire the development of multifunctional membrane systems for more sustainable and energy-efficient enantioseparation.