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Ion implantation is one of the best methods to manufacture silicon-vacancy (SiV) centers in diamond, which can be used as qubits. In this work, molecular dynamics (MD) simulation was conducted to analyze the damage evolution and distribution during the process of silicon ion implantation into bulk diamond and subsequent annealing. Tersoff-ZBL (Ziegler-Biersack-Littmark) potential was used to describe the atomic interaction. Identify Diamond Structure (IDS) and Wigner-Seitz defect analysis methods were used to calculate damages and vacancies. After 2393 K annealing, about 42.5% of ion induced IDS damages were recovered. During the temperature cooling down from 2393 K to 293 K, the movements of silicon atoms along the implantation direction were sensitive to the temperature variation, while vacancies were almost insensitive. MD simulation is helpful to illustrate the ion implant induced damages’ dynamic evolution and Si-V related defects, which can assist a deeper understanding of SiV center’s manufacturing.