The hidden order of atomic packing in amorphous structures and how this may provide the origin of plastic events have long been a goal in the understanding of plastic deformation in metallic glasses. To pursue this issue, we employ here molecular dynamic simulations to create three-dimensional models for a few metallic glasses where, based on the geometrical frustration of the coordination polyhedra, we classify the atoms in the amorphous structure into six distinct species, where “gradient atomic packing structure” exists. The local structure in the amorphous state can display a gradual transition from loose stacking to dense stacking of atoms, followed by a gradient evolution of atomic performance. As such, the amorphous alloy specifically comprises three discernible regions: solid-like, transition, and liquid-like regions, each one possessing different types of atoms. We also demonstrate that the liquid-like atoms correlate most strongly with fertile sites for shear transformation, the transition atoms take second place, whereas the solid-like atoms contribute the least because of their lowest correlation level with the liquid-like atoms. Unlike the “geometrically unfavored motifs” model which fails to consider the role of medium-range order, our model gives a definite structure for the so-called “soft spots”, that is, a combination of liquid-like atoms and their neighbors, in favor of quantifying and comparing their number between different metallic glasses, which can provide a rational explanation for the unique mechanical behavior of metallic glasses.