This study investigates the mechanical behavior of binary Cu-Zr metallic glass under cyclic loading using the molecular dynamics simulation method. Firstly, simulations of single indentation are performed on metallic glasses with four different alloy ratios (Cu₅₀Zr₅₀, Cu₅₄Zr₄₆, Cu₆₀Zr₄₀, and Cu₆₄Zr₃₆), and their corresponding force-depth curves are obtained. The evolution of their microstructures is analyzed using Voronoi indices. To further reveal the hardening mechanism of the metallic glasses under cyclic loading with different alloy ratios and loading rates, the hardness, average atomic volume, residual indentation depth, local shear strain, and large-strain atoms involved in indentation are analyzed. The results indicate that the yield capacity of metallic glass increases with the Cu content under different alloy ratios, primarily due to a higher Cu content resulting in more short-range-ordered structures, thus enhancing the yield capacity. Simulation results also show that after cyclic loading, the average hardness at large-depth indentation of metallic glass with the four different alloy ratios increases by 1.86% to 3.17% compared to that of single indentation. The generation and accumulation of shear bands during the cyclic process, as well as the decrease in the average atomic volume in the region beneath the indenter, lead to a denser structure, effectively resisting further deformation and serving as the main factors contributing to the hardening effect. After cyclic indentation of Cu₅₀Zr₅₀ metallic glass at different loading speeds (80 m/s, 100 m/s, and 150 m/s), it is found that the higher the loading rate, the more micro-plastic deformation, residual indentation depth, and large-strain atoms in the matrix. This leads to a higher average hardness and a more pronounced hardening effect in the metallic glass. This work not only contributes to a better understanding of the plastic deformation mechanism of binary Cu-Zr metallic glass under cyclic loading, but also provides reference data for potential applications and the design of new nanostructured materials.