This work shows the structural evolution of a Au-Sn bimetallic system during the nanoscale diffusion process. Based on X-ray absorption fine structure (XAFS) spectroscopy, X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM) and energy dispersive X-ray spectrometry (EDX), insights were obtained into the detailed composition and structure of the Au-Sn bimetallic system, demonstrating the sequential formation of stable Au/AuSn, AuSn, AuSn/AuSn(2) and AuSn(2) nanocrystals (Au/AuSn and AuSn/AuSn(2) refer to core/shell structures) rather than disordered alloys or alloys with an equal Sn atomic distribution. Furthermore, the formation mechanism of Au-Sn intermetallic compounds and their core/shell structures are discussed. Through elucidating the structural evolution in the diffusion process, we can easily guide the design of other novel bimetallic phases and their core/shell structures which could be predicted between the noble metals (Cu, Ag, Au) and the IIIA or IVA (In, Sn, Pb) metallic elements owing to the rapid diffusion mechanism.