The continuous development of semiconductor quantum dots (QDs) in biochemical research has attracted special attention, and surface functionalizing becomes more important to optimize their performance. Ligand exchange reactions are commonly used to modify the surface of QDs for their biomedical applications. However, the kinetics of ligand exchange for semiconductor QDs remain fully unexplored. Here, we describe a simple and rapid method to characterize the ligand exchange reactions on CdSe/ZnS QDs by capillary electrophoresis (CE). The results of ultraviolet-visible absorption spectra, fluorescence spectra, and Fourier transform infrared spectroscopy indicated the successful implementation of the ligand exchange process. The dynamics of ligand exchange of OA-coated CdSe/ZnS QDs with 4-mercaptobenzoic acid was monitored by CE, and the observed ligand exchange trends were fitted with logistic functions. When the ligand exchange reactions reached equilibrium, the ligand density of QDs can be quantified by CE. It is anticipated that CE will be a new powerful technique for quantitative analysis of the ligand exchange reactions on the surface of QDs.