Room-temperature plasticity in metallic glasses (MGs) is commonly associated with local structural heterogeneity; however, direct observation of the subtle structural change caused by plasticity is vitally important but the data are extremely scarce. Based on dynamic atomic force microscopy (DAFM), here we show that plasticity-induced structural evolution in a Zr-Ni MG can be revealed via nano-scale viscoelastic contacts between an AFM tip and plastically deformed MG surface layers. Our experimental results clearly show a spatial amplification of the nano-scale structural heterogeneity caused by the distributed plastic flow, which can be linked to the limited growth, reorientation and agglomeration of some nano-scale energy-absorbing regions, which are reminiscent of the behavior of the defect-like regions with non-affine deformation as conceived in many theories and models. Furthermore, we are able to experimentally extract the thermodynamic properties of these nano-scale regions, which possess an energy barrier of 0.3-0.5 eV, about half of that for a typical shear transformation event that usually occurs at the onset of plasticity. The outcome of our current work sheds quantitative insights into the correlation between plasticity and structural heterogeneity in MGs.