Electron beam (e-beam) has been developed for nanomaterial observation and moreover to induce structural evolutions in atomic scale. In this work, we demonstrate the deoxidation of cuprous oxide (Cu2O) and the formation of an atomically flat surface on a Cu nanowire by e-beam irradiation. To develop e-beam irradiation applications, the relation between e-beam radiation and the atomic surface is significant. Through the density functional theory simulation of atomic sputtering, an obvious disparity in the sputtering threshold has been found under different structural conditions, which leads to different structural evolutions. Both surface deoxidation and atomic surface flattening reactions have been identified as self-limiting and irreversible processes via in situ transmission electron microscope observation. Under e-beam irradiation, the dynamic mechanism of atomic surface flattening is driven by the convergence of total surface energy and confirmed by climbing-image nudged elastic band (ci-NEB) calculations. With precise control, e-beam irradiation reveals enormous potentials in atomic surface engineering.