Chiral metal nanoclusters stand as pivotal materials in contemporary scientific research, yet their enantiomers predominantly crystallize as racemic mixtures, posing substantial challenges for chirality-based applications. This study elucidates the racemization mechanism in metal nanoclusters and proposes a rational strategy for achieving spontaneous resolution. We demonstrate that racemic cluster assemblies are stabilized in the unit cell by intermolecular interactions between opposite enantiomers; eliminating or diminishing these interactions induces spontaneous resolution, yielding homochiral crystals of either enantiomer. Two illustrative cases are presented: the racemic assembly of Cu 25 H 10 (PhFS) 18 (PPh 4 ) 3 (PhFS = 2-fluorobenzenethiolate) is stabilized by extensive C–H···F hydrogen bonds between enantiomers. Removing fluorine substituents to form Cu 25 H 10 (PhS) 18 (PPh 4 ) 3 (PhS = benzenethiolate) disrupts these interactions and enables resolution. In Cu 4 (PhS) 6 (PPh 4 ) 2, substituting benzene with thiophene ligands (forming R/S–Cu 4 (ThS) 6 (PPh 4 ) 2, ThSH = 2-thiophenethiol) diminishes C–H···π interactions between enantiomers, facilitating spontaneous resolution. Successful resolution is unambiguously confirmed by mirror-image circular dichroism spectra of enantiopure crystals. This study demonstrates the critical role of intermolecular interactions in racemate formation and presents strategies for achieving spontaneous chiral resolution in metal nanoclusters.