Abstract A Zr-based metallic glass is treated by a cryogenic- to room-temperature cycling treatment with 30 cycles. Though the structure after treatment maintains its monolithic amorphous structure, the treated sample exhibits a rejuvenation behavior contrasting with that of an untreated as-cast sample, including a higher relaxation enthalpy and a lower density. The atomic level core-shell heterogeneous microstructure is considered to contribute to the rejuvenation because of the internal stress generated during cycling. The microscopic deformation of the core region by the internal stress may be equivalent to the macroscopic shear band deformation by the external stress, which induces the evolution of the core region and an increased amount of excess free volume. The treated sample also exhibits lower hardness and better plasticity than the untreated sample. A lower shear plane formation energy and larger shear transformation zone volume and size are considered to promote shear band formation and to generate more multiple shear bands to accommodate the plastic deformation. The deep cryogenic cycling treatment is believed to be a feasible and non-destructive way to rejuvenate metallic glass and improve the mechanical properties.