Molecular dynamics simulations were performed to study the deposition of the thermal spraying material under different process parameters. The effects of temperatures, cluster size, and spraying speed on the deposition of Ni clusters on the Fe substrate were examined. The morphology of clusters and the subsurface damage of the substrate were analyzed. The results show that in the heating-up process of Ni cluster, the melting point becomes higher with the increase of cluster size, and the complete melting temperature of Ni cluster is about 1800 K. During the spraying process, the matrix shows a “mountain” shape due to the impact force to disordered atoms. Furthermore, it is also found that spraying speed plays an important role in the deposition process. At lower spraying speed, the flattening ratio decreases again, but at higher spraying speed, the substrate has defects, such as vacancy and atomic cluster after the impact of clusters. Thus, there is a critical spraying speed mechanism in thermal spraying.