Abstract: Nanoparticles of iron oxide and its hydrate were synthesized with hydrothermal method and characterized by infrared, Scanning Electron Microscope (SEM) and soon. The dimensions of the nanoparticles are about 50~120 nm. The form of iron oxide nanoparticles appears to be globosity while its hydrate rod. Amino acids intermingling with the synthesized nanoparticles were crystallized to investigate the space effect of the nanoparticles. The crystalline forms of crystal are different from those of pure amino acid. The positions and width of the nanoparticles'peaks in the infrared spectrum change too. Microscope observation and infrared spectrum results indicate the nanoparticles have changed the internal structure of amino acids crystal. 3-(4, 5-dimethythiazol 2-yl)-2,5 diphenyltetrazolium bromide (MTT) assay was used to determine their cytotoxicity. The Optical Density (OD) value was used to calculate Relative Generation Rate (RGR) of cells. The RGRs of nanoparticles of iron oxide and its hydrate are about 70%~95%, the grades of cytotoxicity are 1~2. This result indicates they just have low toxicity.