The influence of free volume (FV) activation stress on the nanoindentation behaviors of bulk metallic glasses (BMG) Zr65Cu15Al10Ni10 (BMG) was investigated. In this paper, nanoindentation simulations were carried out on samples by the finite element method (FEM) in ABAQUS software using the user-defined material (UMAT), and Berkovich indentation experiments at room temperature were performed on the MG sample at a constant strain rate, to confirm the numerical loading and unloading curves. Based on the measured frictional force by using an atomic force microscope (AFM), we examine the flatness of the tested surface samples to verify the excellent reproducibility of the indentation experiment. The results have shown a good agreement between the experimental and simulated tests. Our simulation results indicated that the FV activation stress has a slight effect on the load-penetration curves. Besides, the plotted contours of numerical data demonstrated that the spatial heterogeneous deformation can be enhanced by severe plastic deformation near the indentation tip. Furthermore, based on the results of the FE modeling contribution, we deduce that the FV activation stress has no remarkable effect on the nanoindentation behavior of Zr-based BMGs, with the exception of a slight improvement in the work hardening of this amorphous material.