Mono-/multivalent ion-selective separation has become a common requirement at the water-energy nexus, including energy storage and conversion, water purification, and sustainable industrial processes. In this review, we summarize the theory of ion transport through membrane and mechanisms of selective ion separation in nanofiltration (NF) briefly. Recent advancing in improving the mono-/multivalent ion selectivity of thin-film composite (TFC) NF membrane via size sieving enhancement, electric charge property regulation and co-enhancement of size sieving and electric charge properties are concluded. What's more, three material classes—surface assembly materials, nanomaterials and biomimetic ion channels are highlighted as candidates for the preparation of ion-selective NF membranes. Lastly, design directions and critical challenges for developing high-selectivity nanofiltration membranes based on the ion-selective mechanisms are provided.