Deformation of metallic glasses is closely related to their microstructures which depend on the composition, processing method, and the size of the materials. This subtle structure-property relation is fairly complex and remains to be explored. Here, we scrutinize the microstructural evolution in relation to the mechanical properties in metallic glass nanowires with the same composition and size but subtle microstructural differences by controlling the preparing process using molecular dynamics simulations. The results suggest that a structural threshold exists for the transformation of deformation mechanisms in metallic glasses: when the structural feature exceeds the threshold, the deformation changes from homogeneous flow to shear localized deformation.