Quantum dots (QDs) are nanoscale inorganic particles generally composed of II–VI and III–V elements. Recently, QDs have received great interest in biological applications because of their unique and fascinating optical properties. In this short review, we introduce the synthesis of luminescent QDs in the aqueous phase and characterize certain fundamental parameters of luminescent QDs synthesized in the aqueous phase by fluorescence correlation spectroscopy (FCS), which include, for example, their dynamic diameters and surface charges. Meanwhile, combining with some ensemble spectroscopy techniques, we applied FCS to investigate the quenching process and mechanism of heavy metal ions (e.g., Ag+) on CdTe QDs, as well as the aggregation and subsequent photoactivation process of 3-mercaptopropionic acid–capping CdTe QDs induced by laser irradiation. Our preliminary results demonstrate that FCS is a sensitive and efficient tool to characterize fluorescent nanoparticles, such as QDs, at the single-molecule detection level.