The rapid cooling of a metallic liquid (ML) results in short-range order (SRO) among the atomic arrangements and a disordered structure in the resulting metallic glass (MG). These phenomena cause various possible features in the microscopic structure of the MG, presenting a puzzle about the nature of the MGs’ microscopic structure beyond SRO. In this study, the nanoscale density gradient (NDG) originating from a sequential arrangement of clusters with different atomic packing densities (APDs), representing the medium-range structural heterogeneity in Zr₆₀Cu₃₀Al₁₀ MG, was characterized using electron tomography (ET) combined with image simulations based on structure modeling. The coarse polyhedrons with distinct facets identified in the three-dimensional images coincide with icosahedron-like clusters and represent the spatial positions of clusters with high APDs. Rearrangements of the different clusters according to descending APD order in the glass-forming process are responsible for the NDG that stabilizes both the supercooled ML and the amorphous states and acts as a hidden rule in the transition from ML to MG.