Abstract Molecular dynamics simulations have been performed to investigate the spontaneous phase transformation of copper nanowires. It is found that the spontaneous phase transformation exhibits distinct dependence on the cross-sectional geometry of the nanowires and can lead to the reconstruction of atoms into different atomistic configurations, e.g., pure hexagonal-close-packed crystals, fivefold deformation twins, and core/shell structures. For single-crystal copper nanowires, the critical cross-sectional size, above which no spontaneous phase transformation can occur, is determined. The physical mechanisms underlying the complicated transformation behavior are analyzed from the viewpoints of energy and stresses.