In this article, a large scale multi-particle molecular dynamics (MD) simulation model was developed to study the dynamic structural changes in single crystal diamond under 5 keV Ga + irradiation in conjunction with a transmission electron microscopy (TEM) experiment. The results show that the thickness of ion-induced damaged layer (~ 9.0 nm)obtained from experiments and simulations has good accordance, which demonstrates the high accuracy achieved by the developed MD model. Using this model, the evolution of atomic defects, the spatial distributions of implanted Ga particles the thermal spike at the very core collision area were analysed. The local thermal recrystallizations observed during each single ion collision process and the increase of the density of the non-diamond phase (mostly sp 2 bonded) at irradiation area are fund to be the underling mechanisms responsible for ion fluence dependent amorphization of diamond observed in previous experiments.