The crystal structure evolution and phase transformation of single-crystal germanium during temperature-assisted nanomachining were investigated using the molecular dynamics method. The differences in surface atomic distribution, material removal volume, subsurface damage depth, surface roughness, and normal cutting force of single-crystal germanium under two different cutting depths at preheating temperatures of 300 K, 450 K, 600 K, 750 K, and 900 K were compared. The results show that with the increase in cutting depth, the material removal amount and subsurface damage depth increase. In addition, as the temperature increases, the thermal softening effect mitigates brittle fracture at low temperatures can reduce the brittle fracture at low temperatures, and the material removal mode also transitions from brittle fracture to plastic shear, which makes the internal stress of the workpiece balanced and thus conducive to forming a better machined surface. However, constrained by the size effect, it is difficult to explain the machining mechanism of single-crystal germanium cutting at the macroscopic level. Therefore, this study innovatively simulated the heating input via temperature control, revealing the machining mechanism of single-crystal germanium cutting at different temperatures from a microscopic perspective. The results show that increasing cutting depth enlarges material removal volume and subsurface damage. More importantly, preheating induces a non-monotonic transition in material removal behavior: from brittle fracture at 300 K to stable plastic shear between 450 K and 750 K, and eventually to thermally induced tearing above 750 K. An optimal processing window is identified—450 K minimizes subsurface damage, while 750 K maximizes removal efficiency. These findings provide quantitative guidance for selecting preheating temperatures in ultra-precision machining of brittle semiconductors.