[en] Highlights: • A model with defects was built. • The mechanism of initial defects on the subsurface damage was elucidated. • The structural evolution of diamond in CMP process was investigated. • The large initial defects impact the quality of machined surface. • Stress concentration appears at the defect edge. Surface defects of materials will deteriorate their mechanical properties and limit the applications. Understanding the effect of surface defects on machining performance remains a challenge. Therefore, it is of paramount significance to insight into the structural evolution and subsurface damage induced by defects. Herein, we construct a polishing model with initial defects to make the simulation more realistic, and elucidate the effects of initial defects on the subsurface damage and structure evolution via ReaxFF molecular dynamics simulations. Simulation results show that the structural evolution starts from defect edge, and the substrate with initial defects will produce more amorphous damage layers compared with the ideal substrate. The thickness of the amorphous damage layer is roughly the same as the depth of the initial defects. Moreover, smaller pit defects have a little effect on the surface morphology. Nevertheless, larger pit defects will cause poor surface quality and more severe subsurface damage. Our simulation results are of significance for further understanding the influence of initial defects on subsequent machining quality and subsurface damage, and provide theoretical support for the processing of diamond from an atomic perspective.