Co@Au core shell nanoparticles(NPs) of different shell thicknesses were fabricated by a combination of the displacement process and the reduction-deposition process in a microfluidic reactor. The effect of the shell thickness on the fine structures(local atom arrangement) of core materials was investigated by X-ray Absorption Near Edge Structure(XANES) and Extended X-ray Absorption Fine Structure(EXAFS).The results indicate that the shell thickness affects the fine structure of the core materials by causing atomic re-arrangement between the hexagonal close pack(hcp) and the face centered cubic(fcc) structure, and forming Co-Au bonds in the core-shell interface. The effect of the shell thickness on the fine structures (local atom arrangement) of core materials was investigated by X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS). The results indicate that the shell thickness affects the fine structure of the core materials by causing atomic re-arrangement between the hexagonal close pack (hcp) and the face centered cubic (fcc) structure, and forming Co-Au bonds in the core-shell interface.