Development of carbon-based structures composed of nanoparticles with different type of orbital hybridization of carbon (sp2, sp3) made it possible to create new substances with advanced biomedical properties, luminescent, and magnetic when the carbon components are modified by lanthanides for the applications in Photodynamic Therapy or Magneto-Resonance Imaging. The presented results are devoted to the synthesis, physical-chemical and synchrotron studies of water-soluble complexes of detonation nanodiamonds (particle size 4–5 nm) and fullerenols Gd@C82(OH)X (X ∼ 30). The association of positively charged diamonds and electro-negative fullerenols created the complexes being stable under heating (25–70 °C) while the assembly of fullerenols with the diamonds carrying negative surface charges was less probable. Small angle scattering of synchrotron radiation revealed the association of diamonds into chain-like structures more stable due to additional linking of diamonds via fullerenols. Due to complexing, fullerenols got magnetic resonance properties of negative contrasting substances for MRI diagnostics. The tests on biological cells showed a low toxicity of complexes which can be used as prospective biomedical materials.