<p>Two-dimensional MoS₂ shows great promise for damage-resistant and adaptive functional devices owing to its intrinsic self-healing capability; however, phase-dependent damage and healing mechanisms remain unclear. Here, molecular dynamics simulations investigate the nano-indentation induced damage evolution and self-healing behavior of multilayer MoS₂ with three phase structures (1T, 2H, and 3R). Load-depth response, interlayer sliding, displacement fields, crack propagation, maximum shear strain, and radial distribution functions reveal the underlying mechanisms. Results show that no cracks occur in the 1T phase, indicating excellent structural integrity. The 2H phase exhibits single-layer fracture or localized cracking, and no crack healing is observed in any of these cases. The 3R phase is prone to long strip-like cracks, most of which undergo partial healing. During healing, interlayer reconstruction induces edge dislocations and pronounced interlayer sliding, highly sensitive to the indenter radius. This study clarifies the phase-dependent damage and self-healing mechanisms of MoS₂ at the atomic scale.</p> Graphical abstract <p></p>