In this study, we investigated a combination of nonaqueous CE with capillary gel electrophoresis to achieve highly efficient analysis of metal nanoclusters. In the nonaqueous capillary gel electrophoresis (NACGE), PVA and hydroxypropyl methylcellulose were dissolved in DMSO. In addition, to enhance the entanglement of the polymer chains, Li+ ions were also added. By employing the PVA-DMSO-Li+ solution, we studied the effects of the molecular weight, the degree of hydrolysis, and the concentration of the polymers and Li+ on the separation. As a result, good separations of standard mononuclear metal complexes and tetrairon nanoclusters were achieved by NACGE.