Fullerenols C60(OH)X and C70(OH)X (X ∼ 30) have been studied in aqueous solutions at the concentrations 0.05–22wt% by X-ray and neutron scattering and using modeling hydroxyls’ arrangements on carbon cages to explain the molecular assembly defined by hydrophobic and hydrophilic interactions of molecules. In the case of C60 quantum chemical calculations minimizing molecular energy for different configurations of OH-groups on the carbon cages showed their preferred localization at C60 spheroids’ equatorial zone and at the opposite poles. However, less symmetric hydroxyls’ localization on C70 molecules was found since hydroxyls do not create closed chains on them. As a result, the molecules C60(OH)X are associated into primary chain-like aggregates (∼20 units, few nanometers in size) more likely in water than the fullerenols C70(OH)X forming similar groups of lower aggregation degree. For C60(OH)X and C70(OH)X the peculiarities in hydroxyls’ grafting affected a coordination of primary groups integrated into secondary and tertiary structures at the distances R ∼ 5 nm and R ∼ 30 nm at the concentrations C > 5wt% and C > 10wt%, respectively. The discovered mechanism of fullerenols’ assembly in water will facilitate their use in chemistry and biomedicine.