The deformation behavior of metallic glasses has been shown in prior studies to be often dependent on its structural state, namely higher energy “rejuvenated” state versus lower energy “relaxed” state. Here, the deformation behavior of thermally rejuvenated Zr-Cu-Al-(Ti) bulk metallic glasses (BMGs) was evaluated. Rejuvenation was achieved by cryogenic thermal cycling with increase of free volume measured in terms of enthalpy of relaxation. Hardness, stiffness, and yield strength of the BMGs were all found to decrease while plasticity increased after rejuvenation. More free volume in the rejuvenated BMG resulted in homogeneous plastic deformation as was evident from the high strain rate sensitivity and more pronounced shear band multiplication during uniaxial compression. Shear transformation zone (STZ) volume was calculated by cooperative shear model and correlated well with the change in structural state after rejuvenation. The enhanced plasticity with the addition of 1 at. % Ti as well as after cryogenic thermal cycling was explained by lower activation energy for shear flow initiation due to increased heterogeneity induced in the system. Molecular dynamics simulation demonstrated that the variation in plastic deformation behavior is correlated with local atomic structure changes.