The inhibitory effects of CdTe/ZnS quantum dots (QDs) modified with 3-mercaptopropionic acid (negatively charged) or cysteamine (positively charged) on the metabolic activity of Escherichia coli were investigated using biological microcalorimetry. Results show that the inhibitory ratio of positive QDs is higher than that of negative QDs. Transmission electron microscopy images indicate that QDs are prone to be adsorbed on the surface of E. coli. This condition disturbs the membrane structure and function of E. coli. Fluorescence anisotropy results demonstrate that positive QDs show a significant increase in the membrane fluidity of E. coli and dipalmitoylphosphatidylcholine (DPPC) model membrane. Furthermore, fluorescence anisotropy values of DPPC membrane in the gel phase decreased upon the addition of positive QDs. By contrast, anisotropy values in the liquid-crystalline phase are almost constant. The change in membrane fluidity is associated with the increased permeability of the membrane. Finally, the kinetics of dye leakage from liposomes demonstrate that the surface charge of QDs is crucial to the interaction between QDs and membrane.