This paper aims to establish a relation between excitation of atomic structure, namely rejuvenation, and plasticity behavior of a Zr-based bulk metallic glass (BMG). The synchrotron X-ray diffraction (XRD) results showed that the cryothermal treatment leads to the rejuvenation in the material which is manifested by the structural disordering and the rearrangement of atomic clusters. It is also revealed that the rejuvenated structure includes more potential sites for shear-banding events during compressive loading. Hence, the homogeneous plasticity improves in the rejuvenated samples, which is recognized by self-organized critical state of serrations in the stress-strain curve and high population of shear bands on the lateral surface of samples. On the other side, heterogeneous structure and high energy barrier for shear transitions in as-cast specimen lead to a semi-brittle failure with low plastic deformation. In general, with the increase in the number of cryothermal cycles, the rejuvenation as well as the non-localized deformation enhance in the BMG.