Copper silicide has been studied in the applications of electronic devices and catalysts. In this study, Cu3Si/Si nanowire heterostructures were fabricated through solid state reaction in an in situ transmission electron microscope (TEM). The dynamic diffusion of the copper atoms in the growth process and the formation mechanism are characterized. We found that two dimensional stacking faults (SF) may retard the growth of Cu3Si. Due to the evidence of the block of edge-nucleation (heterogeneous) by the surface oxide, center-nucleation (homogeneous) is suggested to dominate the silicidation. Furthermore, the electrical transport properties of various silicon channel length with Cu3Si/Si heterostructure interfaces and metallic Cu3Si NWs have been investigated. The observations not only provided an alternative pathway to explore the formation mechanisms and interface properties of Cu3Si/Si, but also suggested the potential application of Cu3Si at nanoscale for future processing in nanotechnology.