Mechanical behavior of a Cu-Zr metallic glass (MG) under cyclic indentation loading is investigated via molecular dynamics simulation. A large-depth indentation after cycling is conducted, and the indentation curves show that hardening behavior occurs with cyclic indentation amplitudes exceeding elastic range. The atomic Von Mises shear strain distributions during the large-depth indentation are investigated, and the pre-existing plastic deformation induced by cyclic indentation is found to be the main contributor to the hardening behavior. By monitoring the atom trajectories and Voronoi atom volume, structure densification and free volume reduction phenomenon are found in the area beneath indenter after cycles. The accumulations of irreversible shear strain during cycling induce the area beneath indenter experience atom structure transition and become densified, thus the sample becomes more resistant to further deformation. In addition, the effects of temperatures and loading rates on the hardening behavior are studied. With higher temperature, more homogenous deformation and plasticity are produced, and then inducing more severe hardening in the MG. While with lower loading rate, the hardening phenomenon is found to be less severe because of the localization of shear strain during cycling. (C) 2017 Elsevier B.V. All rights reserved.