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Microscale experimental techniques are challenging in terms of test time, sample preparation, and resolution. It is also difficult for molecular dynamics (MD) to overcome spatial and temporal limitations. Wyoming sodium montmorillonite was used in this study. Based on the Gay-Berne potential (GB), the unloading properties of clay aggregates under different environmental conditions were simulated using coarse-grained molecular dynamics (CGMD) method. The results showed that for each case, the deformation was closely related to the distribution of the stacks. In particular, the relationship between the total number of stacks and void ratio followed the Boltzmann distribution. At the same time, it was found that the stress states in different cases during unloading depend on the particle orientation. For one-dimensional unloading, the particle arrangements exhibited significant anisotropy, leading to a smaller vertical rebound. Owing to the isotropic compression at 1 atm and lateral confinement, the lateral pressure coefficient (k) is >1 in the atmospheric environment. In contrast, limited lateral expansion caused k to be smaller than 1 in a vacuum. With decreasing confining pressure, a linear increase in the void ratio was observed. During this process, the number of small-sized stacks gradually decreased, accompanied by an increase in the number of large-sized stacks. From 100 MPa to 1 MPa, the longer the unloading path, the smaller the rebound. In the range of 0.1–0.7 MPa, the clay configurations reached equilibrium and the unloading paths had no obvious effects on the distribution of stacks. This work demonstrates the validity of the GB potential model, which provides a basis for bottom-up mechanical prediction of the hierarchical structure of Na-montmorillonite particles. [Display omitted] • The effects of environments and loading conditions on the rebound were obvious. • The relationship between N t and void ratio followed the Boltzmann distribution. • Changes in lateral stresses were mainly determined by particle orientation. • Gay-Berne potential reliably reproduce the unloading process of clay aggregates. [ABSTRACT FROM AUTHOR]