Three-dimensional Au structures on bare and organic-compound-modified TiO2(110) surfaces were interrogated by Au L3-edge polarization dependent total reflection fluorescence X-ray absorption fine structure (PTRF-XAFS) spectroscopy. On the bare TiO2(110) surface, icosahedral Au55 nanoclusters were the main product found. When the surfaces were modified with ortho or meso mercaptobenzoic acid (o-MBA or m-MBA), Au was atomically dispersed. Sulfur atoms in the o- and m- MBA formed strong covalent bonds with Au to produce stable Au-MBA (o- and m- forms) surface complexes. On the other hand, only oxygen atoms on the surface did not make a strong enough interaction to stabilize the Au species. We discuss how the Au species formed on the modified TiO2(110) surface and the possibility to control the Au structure by the surface modification method.