The effects of Al2O3, TiO2, and ZnO nanoparticles (NPs) on bacteria cells and bacterial surface biomolecules were studied by Fourier transform infrared (FTIR) spectroscopy. All the examined biomolecules showed IR spectral changes after NP exposure. Lipopolysaccharide and lipoteichoic acid could bind to oxide NPs through hydrogen bonding and ligand exchange, but the cytotoxicity of NPs seemed largely related to the function-involved or devastating changes to proteins and phospholipids of bacteria. The three NPs decreased the intensity ratio of beta-sheets/alpha-helices, indicating protein structure change, which may affect cell physiological activities. The phosphodiester bond of L-a-phosphatidylethanolamine was broken by ZnO NPs, forming phosphate monoesters and resulting in the highly disordered alkyl chain. Such damage to phospholipid molecular structure may lead to membrane rupture and cell leaking, which is consistent with the fact that ZnO is the most toxic of the three NPs. The cell surface biomolecular changes revealed by FTIR spectra provide a better understanding of the cytotoxicity of oxide NPs.