Rejuvenation is a desirable structural excitation process that could improve the deformability of metallic glasses (MGs). Here we evaluate the rejuvenation processes of MG models under cyclic elastic loading by molecular dynamics simulations. Interestingly, the simulation result shows rejuvenation of the MG models enhanced effectively with increased cyclic number and eventually reached a saturated regime. To interpret the two-regime rejuvenation, a new method, atomic computer tomography (ACT) was proposed herein to evaluate the atomic packing density and its distribution of the simulated MGs. Different from those well-documented models proposed previously, three distinctive kinds of regions with various atomic packing densities were identified via ACT evaluation. The atomic packing density transitions among the three kinds of regions upon cyclic elastic loading were proposed to be responsible for both the accumulated and saturated rejuvenation processes, which consisted with the simulated tensile deformation behavior. Our findings may help connecting atomic structure evolution and rejuvenation process in MGs and demonstrating the existence of rejuvenation threshold under cyclic elastic loading.