Nickel-based superalloy GH4169 is widely used as an important material in the aviation field. The rolling forming process can improve its surface quality and performance. Therefore, conducting an extensive investigation into the microscopic plastic deformation defect evolution process of nickel-based single crystal alloys during the rolling process is crucial. This study can offer valuable insights for optimizing rolling parameters. In this paper, a nickel-based superalloy GH4169 single crystal alloy was rolled at different temperatures from the atomic scale using the molecular dynamics (MD) method. The crystal plastic deformation law, dislocation evolution and defect atomic phase transition under different temperature rolling were studied. The results show that the dislocation density of nickel-based single crystal alloys increases as the temperature increases. When the temperature continues to increase, it is accompanied by an increase in vacancy clusters. When the rolling temperature is below 500 K, the atomic phase transition of the subsurface defects of the workpiece is mainly a Close-Packed Hexagonal (HCP) structure; when the temperature continues to increase, the amorphous structure begins to increase, and when the temperature reaches 900 K, the amorphous structure increases significantly. This calculation result is expected to provide a theoretical reference for the optimization of rolling parameters in actual production.