The creep behavior of net-like red soils mainly depends on the micromechanical behavior of clay mineral atoms at the nanoscale. The 1M-tv configuration of illite determined by the experiments of XRD and SEM-EDS, was utilized to address the mechanical properties along various loading directions using the conventional molecular dynamics (MD) simulation method. Furthermore, a novel MD simulation method based on transition state theory was proposed to discuss temperature effects. Simulated results indicate that the ultimate stress value under tensile perpendicular to the illite layer is minimal relative to the transverse direction, the in-plane shear has more resistance to overcome than the transverse shear. Amounts of the tensile, compressive, and shear strengths of illite decrease with increasing temperature, while the strain of steady-state creep at the same loading applied time increases with the temperature. An energy barrier to enter the accelerated creep destruction phase is about 18 kcal/mol. Moreover, the improved MD simulation method can extend the time scale from 200 ps to 186 days. These results may conclude that the proposed MD simulation method may provide a powerful tool to investigate the creep behaviors of clay minerals at experimentally relevant timescales at the nanoscale.