We have developed an advanced centrifugal microsystem which has a capability of automatic and programmed chemical reagent loading and multiplex chemical reactions to screen the colloidal nanocrystal synthesis in a high-throughput manner. As a proof of concept, thirty synthetic reactions for water-soluble multi-color CdS nanocrystals were executed on a chip under ten different conditions. By tuning the concentration of sulfur in a control solution, the CdS nanocrystals in the reaction chambers produced multi-color from green to red depending on the molar ratios of Cd<sup>2+</sup> to S<sup>2-.