Subsurface damage that is caused by mechanical machining is a major impediment to the widespread use of hard–brittle materials. Ultrasonic vibration-assisted macro- or micromachining could facilitate shallow subsurface damage compared with conventional machining. However, the subsurface damage that was induced by ultrasonic vibration-assisted nanomachining on hard–brittle silicon crystal has not yet been thoroughly investigated. In this study, we used a tip-based ultrasonic vibration-assisted nanoscratch approach to machine nanochannels on single-crystal silicon, to investigate the subsurface damage mechanism of the hard–brittle material during ductile machining. The material removal state, morphology, and dimensions of the nanochannel, and the effect of subsurface damage on the scratch outcomes were studied. The materials were expelled in rubbing, plowing, and cutting mode in sequence with an increasing applied normal load, and the silicon was significantly harder than the pristine material after plastic deformation. Transmission electron microscope analysis of the subsurface demonstrated that ultrasonic vibration-assisted nanoscratching led to larger subsurface damage compared with static scratching. The transmission electron microscopy results agreed with the Raman spectroscopy and molecular dynamic simulation. Our findings are important for instructing ultrasonic vibration-assisted machining of hard–brittle materials at the nanoscale level.