In this work, we found two hydrophilic interaction liquid chromatography (HILIC) columns for high-performance liquid chromatography (HPLC) suitable for the high-resolution separation of hydrophilic metal clusters. The mass distributions of the product mixtures of hydrophilic metal clusters were evaluated via HPLC mass spectrometry (LC/MS) using these HILIC columns. Consequently, we observed multiple clusters that had not been previously reported for glutathionate (SG)-protected gold clusters (Aun(SG)m). Additionally, we demonstrated that Aun-xMx(SG)m alloy clusters (M = Ag, Cu, or Pd) in which part of the Au in the Aun(SG)m cluster is replaced by a heteroelement can be synthesized, similar to the case of hydrophobic alloy clusters. It is easy to evaluate the mass distributions of hydrophilic metal clusters using this method. Thus, remarkable progress in the synthesis techniques of hydrophilic metal clusters through the use of this method is anticipated, as is the situation for hydrophobic metal clusters.