Due to the high importance of transferrin in targeting tumor, the investigation on the functionalization process of quantum dots (QDs) using transferrin is very essential. In this paper, the interaction between CdSe and CdSe@ZnS QDs with transferrin was studied by various spectroscopies. It was found that the two types of QDs triggered the fluorescence quenching of transferrin by the static quenching mechanism. At 298 K, the binding constant for CdSe@ZnS QDs (8.03 × 106 L·mol−1) is higher than CdSe QDs (2.84 × 106 L·mol−1), implying that CdSe@ZnS QDs could bind stronger to transferrin. In addition, the values of enthalpy change (∆H), entropy change (∆S) and Gibbs free energy change (∆G) were negative, indicating that the binding procedures between both QDs and transferrin were spontaneous and the main binding forces were hydrogen bonding and van der Waals force. The results of CD spectra indicated that both QDs induced the conformational change of transferrin, which further caused the release of iron ions from transferrin. Compared with CdSe QDs, less contents of iron ions in transferrin were detected after interaction with CdSe@ZnS QDs. Additional cytotoxicity tests showed that both QDs were toxic to Hela and 293T cells, but the cytotoxicity of CdSe QDs was stronger than that of CdSe@ZnS QDs. Moreover, the combination of transferrin failed to promote the cytotoxicity of CdSe QDs and CdSe@ZnS QDs, which is ascribed to the release of iron ions during the interaction process between QDs and transferrin.