In this paper, molecular dynamics method with the Tersoff-ZBL combined interatomic potential was adopted to study the dynamics of focused ion beam (FIB) milling and subsequent annealing. The Ga FIB induced damage and its recovery mechanism during subsequent annealing process were investigated in nanoscale time and space. To investigate the nanoscale damage during FIB milling with the ion energy of 0.5 keV, 1 keV and 2 keV, radial distribution function, bond length distribution, bond angle distribution, and common neighbour analysis (CNA) were calculated and analyzed under various ion doses. FIB irradiated silicon substrate with ion dose of 2 x 10(14) ions/cm(2) was annealed at various annealing temperatures from 1400K to 2400K. Molecular dynamics simulation illustrated that as a-Si region was surrounded by c-Si after implantation, the recrystallization lead to a c-Si regrowth processes both from bottom towards top surface and from periphery to centre. The damage area profiles by CNA represented a shortest recovery time of 2.0 ns at 2200 K. Both melting on the top surface and recrystallization at crystalline/amorphous interface have existed as annealing at 2400 K, which is near the melting point. Ga migrated together and moved towards the surface with the a-Si/c-Si interface. (C) 2015 Elsevier B.V. All rights reserved.