The biocompatibility of nanomaterials is closely related to their morphologies, defects, surface properties and impurities. In this manuscript, hydrochloric acid and nitric acid solution were adopted to purify and oxidize boron nitride nanotubes (BNNTs). The as prepared hydroxylated BNNTs (BNNTs-OH) were characterized by XPS, FTIR, TG, TEM, Zeta Potential and Photoluminescence. Results showed that BNNTs were successfully oxidized and hydroxylation occurred at the B site. BNNTs-OH had good dispersibility in aqueous solution, and the average hydration substitution was about 1246.7nm. The special fluorescence characteristics could realize the location of BNNTs inside the cells under a certain excitation wavelength. Cytotoxicity tests showed that BNNTs-OH had no cytotoxicity on L02 cells, a human embryonic liver cell line, demonstrating that BNNTs could be a kind of biocompatible nanomaterial and had promising applications in biomedical field.