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In this study, the process of diamond abrasive polishing monocrystalline silicon with circular inclusions was simulated by molecular dynamics. The variation in coordination number, polishing force, friction coefficient, potential energy, polishing temperature, and dislocation were analyzed and studied by changing the size of inclusions in monocrystalline silicon. The analysis of coordination number indicates that the number of silicon atoms with the coordination number of five increases with increasing inclusions, and the atoms mainly gather at the bottom of inclusions; the larger the inclusions, the deeper the subsurface damage; but after polishing, large inclusions increased the number of defective atoms recovered; the analysis of diamond structure revealed that the increase in the diameter of inclusions increases the number of damaged diamond structure atoms. The results show that the polishing force, normal force, and friction coefficient increase with increasing circular inclusion, but the effect of the size of the inclusion on the temperature is not significant; the potential energy of the system first increases obviously and then decreases slowly after reaching the peak; the number and length of dislocations decrease to 0 at first and then increase gradually.