Fullerenes are novel carbon nanomaterials that hold great promise in diverse areas, but the limited solubility make them hardly dispersible in aqueous environment and the applications in hydrophilic systems are restricted, in particular for biomedical areas. Currently, chemical functionalization is the main approach to increase the hydrophilicity of fullerenes, where the soluble fullerene derivatives show lower toxicity and interesting bio-effects. Among these fullerene derivatives, hydroxylated fullerene (fullerenol) has good biocompatibility, antitumor activity, antivirus activity, antioxidation activity and photosensitive activity, thus is widely studied and applied. The structure and functionalization of fullerenol determine the bio-effects in biomedical applications. However, the structure of fullerenol is very complicated and the precise structure of fullerenol has not been achieved yet, such as the hydroxyl group number, the position of functional groups and the chemical forms of surface groups. Herein, we adopted 13C staple isotope labeling to investigate the chemical structure of fullerenol. 13C-skeleton labeled fullerene C60 was prepared by arc discharge method. Then, 13C-C60 was hydroxylated by tetrabutylammonium hydroxide (TBAH) amine alkali catalysis-oxidation to obtain 13C-fullerenol. The 13C-fullerenol was characterized by TOF-MS, IR, X-ray photoelectron spectroscopy (XPS), NMR to analyze the structure of fullerenol. The results indicated that 13C atoms were labeled on the skeleton of fullerene cage. Hydroxylation did not break the carbon cage, which was reflected by the strong C60 peak in the TOF-MS spectrum. The Poisson distribution of mass spectra indicated the isotopic effects and the skeleton labeling by 13C. Based on the TOF-MS, there were about five 13C atoms on each fullerene cage. The higher mass signals were assigned to the oxidized fullerene cage and the lack of very large mass signal suggested the detachment of functional groups during the laser irradiation. The oxygen containing groups were confirmed by IR spectrum. A 3340, 1372 and 1074 cm - 1 peaks were attributed to be C−O/C−OH groups. XPS analyses indicated the chemical components of fullerenol as C 76%−82%, O 14%−18% and Na 0.6%−4%. The C 1s XPS spectra were divided into three major components, namely 284.56−284.86 eV for pristine carbon, 286.07−286.38 eV for C−O and 288.57−288.82 eV for C=O. Based on these, the chemical formulation of fullerenol was defined as Na n +[C60O x (OH) y ] n - , where the oxidation degree of fullerenol was regulated by the alkali concentration. The 1H NMR spectrum showed signals at δ 1.23, 2.50 and 3.34. Only the weak peak at δ 1.23 was due to hydroxyl groups of fullerenol, the rest signals were due to water and dimethyl sulphoxide (DMSO). Enhanced 13C NMR signals were observed at δ 175, 137 and 75−80, which were assigned to C=C−O, C=C and C−OH. Other weak signals were found at δ 160 for O=C−OH, δ 100 for RO−RCH−OH or RO−R1CR2−OH and δ 54 for C atoms in epoxy structure. In conculsion, the structure of 13C-fullerenol was explore to reach the formula of Na n +[C60O x (OH) y ] n - and the exact numbers depended on the reaction parameters during the hydroxylation. 13C isotope labeling largely enhanced the 13C-NMR signals and revealed the intact fullerene cage during the hydroxylation according to the TOF-MS. The complicated surface functional groups were relfected by IR, XPS and NMR, where multiple forms were identified as hemiacetal/hemiketal groups, epoxy groups, carboxylic ester, carbonyl groups, and so on. The results would definitely benifit the ongoing exploration of fullerenol bio-effects/bioapplications and structure-activity relationship. The 13C labeled fullerene and fullerenol could be used for the quantification of carbon nanomaterials in biological systems.