This report describes the precise and systematic synthesis of PdAu24 clusters protected with two types of thiolate ligands (-SR1 and -SR2). It involved high-resolution separation of metal clusters containing a distribution of chemical compositions, PdAu24(SR1)(18-n) (SR2)(n) (n = 0, 1, 2,..., 18), to individual clusters of specific n using high-performance liquid chromatography. Similar high-resolution separation was achieved for a few ligand combinations as well as clusters with other metal cores, such as Au-25 and Au-38. These results demonstrate the ability to precisely control the chemical composition of two types of ligands in thiolate-protected mono- and bimetallic metal clusters. It is expected that greater functional control of thiolate-protected metal clusters, their regular arrays, and systematic variation of their properties can now be achieved.