Molecular dynamics simulations and dynamic mechanical analysis experiments were employed to investigate the mechanical behavior of metallic glasses subjected to iteration deformation in a nominally elastic region. It was found that cyclic deformation leads to the formation of irreversible shear transformation zones (STZs) and a permanent uniform strain. The initiation of STZs is directly correlated with the atomic heterogeneity of the metallic glass and the accumulated permanent strain has a linear relation with the number of STZs. This study reveals a new deformation mode and offers insights into the atomic mechanisms of STZ formation and low temperature uniform plastic deformation of metallic glasses.