In this work, a facile ion-pairing strategy for asymmetric synthesis of optically active negatively charged chiral metal nanoparticles using chiral ammonium cations is demonstrated. A new thiolated chiral three-concentric shell cluster, [Ag28Cu12(SR)(24)](4-), was first synthesized as a racemic mixture and characterized by single-crystal X-ray structure determination. Mass spectrometric measurements revealed relatively strong ion-pairing interactions between the anionic nanocluster and ammonium cations. Inspired by this observation, the as-prepared racemic mixture was separated into enantiomers by employing chiral quaternary ammonium salts as chiral resolution agents. Subsequently, direct asymmetric synthesis of optically active enantiomers of [Ag28Cu12(SR)(24)](4-) was achieved by using appropriate chiral ammonium cations (such as N-benzylcinchoninium vs N-benzylcinchonidinium) in the cluster synthesis. These simple strategies, ion pairing enantioseparation and direct asymmetric synthesis using chiral counterions, may be of general use in preparing chiral metal nanoparticles.