In this paper, molecular dynamics simulations are carried out to investigate the cutting mechanism during the hybrid machining process combined the thermal and vibration assistants. A modified cutting model is applied to study the material removal behavior and subsurface damage formation in one vibration cycle. The results indicate that during the hybrid machining process, the dominant material removal mechanism could transform from extrusion to shearing in a single vibration cycle. With an increase of the cutting temperature, the generation and propagation of cracks are effectively suppressed while the swelling appears when the dominant material removal mechanism becomes shearing. The formation mechanism of the subsurface damage in one vibration cycle can be distinct according to the stress distribution. Moreover, the generation of the vacancies in workpiece becomes apparent with increasing temperature, which is an important phenomenon in hybrid machining process.