Characterizing the microstructural heterogeneity of metallic glasses (MGs) remains a key challenge in materials science, as existing experimental and computational techniques lack the ability to resolve atomic-scale localized structural features. This gap hinders understanding of how heterogeneity governs MG plastic deformation, which is driven by shear transformation zones (STZs)—nanoscale regions of collective atomic rearrangement. To address this, we introduce three-dimensional atomic density tomography (3D-ACT), a technique that quantifies local atomic packing density at 1 Å resolution via a 3.5 Å spherical probe (with "ACT value" defined as atomic count within the probe). Using a validated threshold of ACT < 9 (identified via maximum disparity in low-density region fractions), we precisely map potential STZs. We applied 3D-ACT to molecular dynamics (MD) simulations of Al₉₀Sm₁₀ MGs fabricated at 0.1, 1, and 10 K/ps. Extracting five key STZ parameters (total count, cluster count, average cluster size, size variability, spatial uniformity) revealed that 1 K/ps (moderate cooling) yields an optimal STZ network: uniform dispersion, balanced cluster sizes, and moderate connectivity. We developed a comprehensive evaluation index (I) weighted by parameter-plasticity correlations. Uniaxial tensile MD simulations confirmed the 1 K/ps sample exhibits the highest plasticity due to synchronized STZ activation and distributed shear bands. Higher or lower cooling causes STZ aggregation or dispersion, respectively, reducing deformation stability. This work establishes 3D-ACT as a robust tool for STZ analysis, links microstructural heterogeneity to macroscopic properties, and provides a framework for designing high-toughness MGs by tuning STZ dynamics.