Because the synthesis of metal clusters with multiple ligand types results in a distribution of ligands, high-resolution separation of each unique cluster from the mixture is required for precise control of the ligand composition. Reverse-phase high-performance liquid chromatography combined with appropriate transitioning of the mobile phase composition is an extremely effective means of separating ligand combinations when working with metal clusters protected by two different types of thiolates. We report herein advanced use of this method. The studies involving Au₂₄Pd(SR₁)₁₈-x(SR₂)x and Au₂₄Pd(SR₁)₁₈-x(SeR₂)x (SR₁, SR₂ = thiolate, SeR₂ = selenolate) revealed the following. (1) In general, an increase in the difference between the polarities of the functional groups incorporated in the two types of ligands improves the separation resolution. A suitable ligand combination for separation can be predicted from the retention times of Au₂₄Pd(SR₁)₁₈ and Au₂₄Pd(SR₂)₁₈, which cause the terminal peaks in a series of peaks. (2) The use of a step-gradient program during the mobile phase substitution results in improved resolution compared to that achievable with the linear gradients applied in prior work. (3) This technique is also useful for the evaluation of the chemical compositions of metal clusters protected by two different types of ligands with similar molecular weights. These findings will provide clear design guidelines for the functionalization of metal clusters via control of the ligand composition, and will also improve our understanding of the high-resolution isolation of metal clusters.