The establishment of the cluster-based structure-property relationship is of great significance to enhance the mechanical properties of metallic glasses (MGs). In this paper, molecular dynamics simulation has been used to obtain the uniaxial compression deformation process at four cooling rates. The results show that the molar volume and atomic average packing density increase with the increase of the cooling rate. The yield strength decreases, and the deformation mode gradually changes from localized deformation to delocalized deformation. The increase of icosahedron and icosahedron-like within the system impedes the plastic flow of MGs. The large-sized nanoclusters composed of icosahedron and icosahedron-like are destroyed during compression, resulting in a concentration of stress localization. The system has high initial resistance to plastic flow. The shear transition zone is concentrated to form shear bands, which reduces the plasticity of MGs. These results have marvelous theoretical guidance for improving the plasticity of MGs.