To uncover the physical correlation between intrinsic structural heterogeneity and mechanical properties of metallic glasses, we performed high-pressure torsion (HPT) to tailor their microstructure with a rejuvenated state. Nanoindentation results show that the change of mechanical properties results from the convolution of the intrinsic thermal activation process and the structural inhomogeneity in the glassy phase. The spatial heterogeneity induced by severe plastic deformation can markedly operate to reduce the energy barrier for shear transformation zone (STZ) activation and increase the number of STZ events during tensile testing to accommodate the plastic strain, leading to a brittle-to-ductile transition. We highlight that by properly controlling the distribution of structural heterogeneities, one can purposely tune the mechanical performance of metallic glasses.