In recent years, the exploration of concealed deposits has become extremely urgent as the shortage of surface resources worsens. In this study, naturally formed nanoparticles in five media (deep-seated fault gouge, ascending gas flow, soil, shallow groundwater and deep groundwater) in Chaihulanzi Au deposit, China, were analyzed by transmission electron microscopy. The characteristics of category, shape, lattice parameters, chemical component and association were obtained. The results show that deep media can carry natural nanoparticles to the surface media, resulting in an increased proportion of O and metal chemical valence such as Pb and Cu in nanoparticles. The metal elements Au, Ag, Cu, Zn and As in nanoparticles correspond to those of orebody minerals. Au-Ag-Cu, Fe-As, Cu-Sn and Pb-Zn element associations in nanoparticles are similar to those of mineral composition or orebody paragenesis in Chaihulanzi deposit. Compared with nanoparticle characteristics in deposit and background areas, it can be deduced that natural ore-bearing nanoparticles come from concealed orebodies. With the characteristics of more oxide forms and the dislocation of the crystal lattice, these nanoparticles are formed by faulting and oxidation. Nanoparticles produced in concealed orebodies that migrate from the deep to the surface media could be used for prospecting.