The deposition of Ni film on the Si substrate is important due to its broad applications in electronics, especially at the nanoscale. In this study, we applied molecular dynamics simulations to perform a subatomic observation simultaneously during the process of sputtering Ni on crystalline Si, and a model according to the Thompson formula was developed to simulate the energy distribution of ejected atoms during sputtering. We found the critical parameters controlling interdiffusion behavior were substrate temperature and incident flux of Ni. The substrate temperature significantly leads the crystallinity of the Ni film, where they exhibit amorphous, FCC, and BCC structures at substrate temperatures below 400, 500−600, and beyond 700 K, respectively. The incident flux dominates the crystallinity of the deposited Ni film. Only amorphous Ni forms with 10 atom/ps flux, and fewer defects in the FCC Ni film were observed with 2.5 atom/ps flux. To balance the throughputs and film quality, an incident flux of 2.5 atom/ps is the optimized choice. The detailed understanding enables the control of thin films during electronic fabrication.