An effective capillary electrophoretic technique for separating samples of negatively charged, polydisperse, water-soluble gold monolayer-protected cluster (Au MPC) protected by monolayers of N-aCetyl-L-cysteine has been developed. The separation mechanisms of the Au MPC in CZE suggest that the larger core sizes Au MPC emerge first from the capillary The electrophoretic separation depends on pH, buffer concentration, and organic modifiers. The addition of aliphatic: alcohols to the ran buffer can improve the separation of Au MPC by reducing the EOF and changing the selectivity between the Au MPCs. The enhancement of resolution is attributed to the more significant difference in the charge-to-size ratio between the Au MPCs. The run buffer containing 20 v/v % ethanol provides the best separation for water-soluble Au MPC. Our proposed CE method provides a powerful tool to evaluate and separate the water-soluble Au MPC products.