Quantitatively correlating the amorphous structure in metallic glasses with their physical properties has been a long-sought goal. Here we introduce “flexibility volume” as a universal indicator of the structural state, to correlate with properties on both atomic and macroscopic levels. The flexibility volume is assessed via atomic vibrations that probe local space and interactions, measurable both computationally and experimentally. This indicator deterministically predicts the shear modulus, which is at the heart of key properties of MGs. The flexibility volume correlates strongly with atomic packing topology, and with the activation energy for thermally activated relaxation or the propensity for stress-driven shear transformations, providing a structural underpinning of the mechanical heterogeneities. The concrete structure-property correlations discovered are robust and prognostic for all compositions, processing conditions and length scales. We advocate flexibility volume as a single-parameter indicator, in lieu of the widely cited“free volume”, in understanding the structural state and properties of MGs.