The origin of the deformation in metallic glasses is attributed to rearrangements of atoms in some structurally weak spots behaving as flow units, which are associated with free volumes. In the present study, Xe-ion beam is used to manipulate the free-volume fraction, and influence on the mechanical behavior of a Zr-based metallic glass. The irradiation at low dosages can change the structure by increasing the free volume, and by homogenising the distribution of free volume. The increase in the free-volume fraction is equivalent to the increase in the deformation temperature, thus resulting in the decrease in the yield strength. The analysis of stochastic strain burst size in the metallic glass irradiated at different dosages indicates that the strain burst depends on the yield strength and homogeneity of the glassy phase. The results of this study highlight the fact that the quantitative manipulation of the homogeneity and the amount of free volumes can be achieved through low-dose ion irradiation, which can modify the mechanical behavior of metallic glasses.