Some nanoparticles, such as quantum dots (QDs), are widely used in the biological and biomedical fields due to their unique optical properties. However, little is currently known about the interaction between these nanoparticles and biomolecules. Herein, we systemically investigated the interaction between chaperonin GroEL and water-soluble CdTe QDs based on fluorescence correlation spectroscopy (FCS), capillary electrophoresis, and fluorescence spectrometry. We observed that some water-soluble CdTe QDs were able to enter the inner cavity of GroEL and formed an inclusion complex after the activation of chaperonin GroEL with ATP. The inclusion of GroEL was size-selective to QDs and only small QDs were able to enter the inner cavity. The inclusion could suppress the fluorescence quenching of the QDs. Meanwhile, we evaluated the association constant between chaperonin GroEL and CdTe QDs by FCS. Our results further demonstrated that FCS was a very useful tool for study of the interaction of QDs and biomolecules.