When illuminated by near-UV light, titanium dioxide (TiO2) exhibits excellent bactericidal activity. However, there exist some different mechanisms for cell killing via photocatalysis. In the present study, the photocatalytically bactericidal mechanism of TiO2 thin films was investigated by atomic force microscopy (AFM) in conjugation with some other techniques. The decomposition process of the cell wall and the cell membrane was directly observed by AFM for the first time. The resultant change in cell permeability was confirmed by potassium ion (K+) leakage. Quantum dots (QDs) were designed originally as a probe to examine the cell permeability for macromolecules. The corresponding bactericidal activity of TiO2 thin films was examined by cell viability assay. These results suggested that the cell death was caused by the decomposition of the cell wall and the cell membrane and the resultant leakage of intracellular molecules.