Understanding the time-dependent behaviour of calcium silicate hydrates (C-S-H) under stresses is crucial for unraveling the microscopic creep behavior of concrete and its consequences on the evolution of nanostructure of C-S-H. In this study, the structural evolution of C-S-H nanostructure under stress was investigated using reactive molecular dynamics and stress perturbation technique. Under sustained stress, C-S-H nanostructure undergoes a relaxation process leading to a creep deformation and transitioning the system towards a more energetically stable state. The process was comprehensively examined under shear stress through a detailed analysis of the system's potential energy. A hardening phenomenon was observed within calcium silicate layers throughout this relaxation process, categorizing in three distinct stages. in Stage I, structural reorganization occurred in the silicate chains, progressing towards a stable state by reducing non-bonded interactions. The calcium-oxygen ionic bonds within the intralayer were strengthened in Stage II, leading to a decrease in bonding energy. Finally, the interface between calcium silicate layers and the interlayer contributed to overall structural stability in StageIII.