Due to its appealing characteristics, molybdenum disulfide (MoS2) presents a promising avenue for the exploration of lubrication protection materials in high-energy irradiation scenarios. Herein, we present a comprehensive investigation into the defect behavior of multilayer MoS2 under argon (Ar) atom irradiation leveraging molecular dynamics simulations. We have demonstrated the energy shifts and structural evolution in MoS2 upon irradiation, including the emergence of Frenkel defects and intricate defect clusters. The structural damage exhibits an initial increase followed by a subsequent decrease as the incident kinetic energy increases, ultimately peaking at 2.5 keV. Moreover, we investigated the effect of postannealing on defect recovery and conducted the uniaxial tensile and interlayer shearing simulation in order to provide valuable insights for the defect evolution and its impact on mechanical and tribological properties. Furthermore, we have proposed the optimal annealing temperature. The current study reveals the atomic mechanisms underlying irradiation-induced damage on the structural integrity and mechanical performance of MoS2, thereby providing crucial guidance for its vital application in nuclear reactors and aerospace industries.