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The bulk metallic glasses (BMGs) are potential metallic materials due to their interesting properties, such as the high strength, high elastic strain limit, and high wear/corrosion resistance. Over the past four decades, a variety of studies have been done on the characteristics of the mechanical, thermodynamic properties of such category of metallic materials, but there still remain many questions about basic deformation mechanisms and their microstructures so far. Molecular dynamics (MD) simulation can provide significant insight into material properties under the atomic level and see a detailed picture of the model under available investigation in explaining the connection of macroscopic properties to atomic scale. MD simulation is applied to study the material properties and the deformation mechanisms in various binary metallic glasses and intended to examine the feasibility of MD simulation to compare the experimental results obtained in our laboratory over the past few years. The gradual vitrification evolution of atom mixing and local atomic pairing structure of the binary Zr-Ni, Zr-Ti alloys and pure Zr element during severe deformation at room temperature is traced numerically by molecular dynamic simulation. It is found that the icosahedra clusters will gradually develop with the increasing of disorder environment of alloys in the Zr-Ni, Zr-Ti systems, forming amorphous atomic packing. Other compound-like transition structures were also observed in transient in the Zr-Ni couple during the solid-state amorphization process under severe plastic deformation. The crystalline pure Zr can be vitrified in the simulation provided that the rolling speed is high enough and the rolling temperature is maintained at around 300 K. On the other hand, the effective medium theory (EMT) inter-atomic potential is employed in the molecular dynamics (MD) simulation to challenge the study of the diffusion properties in the Mg-Cu thin films. The transition of local structures of Mg-Cu thin films is traced at annealing temperatures of 300, 413, and 500 K. Furthermore, the simulation results are compared with the experimental results obtained from the transmission electron microscopy and X-ray diffraction. The gradual evolution of the local atomic pairing and cluster structure is discussed in light of the Mg and Cu atomic characteristics. Lately, the progress of the cyclic-fatigue damage in a binary Zr-Cu metallic glass in small size scale is investigated using classical molecular-dynamics (MD) simulations. The three-dimensional Zr-Cu fully amorphous structure is produced by quenching at a cooling rate 5 K/ps (ps = 10-12 s-1) from a high liquid temperature. The Nose-Hoover chain method is used to control the temperature and pressure to maintain a reasonable thermodynamic state during the MD-simulation process, as well as to bring the imposed cyclic stress on the subsequent simulation process. Both the stress- and strain-control cyclic loadings are applied to investigate the structural response and free-volume evolution. The overall structure would consistently maintain the amorphous state during cyclic loading. The plastic deformation in simulated samples proceeds via the network-like development of individual shear transition zones (STZs) by the reversible and irreversible structure-relaxations during cyclic loading, dislike the contribution of shear band in large-scale specimens. Dynamic recovery and reversible/irreversible structure rearrangements occur in the current model, along with annihilation of excessive free volumes. This behavior might be able to retard the damage growth of metallic glass and enhance their fatigue life.