Understanding the atomic diffusions at the nanoscale is important for controlling the synthesis and utilization of nanomaterials. Here, using in situ X-ray absorption spectroscopy coupled with theoretical calculations, we demonstrate a so far unexplored unidirectional diffusion from the Au shell to the Cu core in thermally alloying Cu@Au core@shell architecture of ca. 7.1 nm. The initial diffusion step at 423 K is found to be characterized by the formation of a diffusion layer composed of a Au-dilute substitutional CuAu-like intermetallic compound with short Cu-Au bond length (2.61 Å). The diffusion further happens by the migration of the Au atoms with large disorder into the interior Cu matrix at higher temperatures (453 and 553 K). These results suggest that the structural preference of a CuAu-like compound, along with the nanosized effect, plays a critical role in determining the atomic diffusion dynamics.