Due to its extremely high optical uniformity and excellent hot stability, glass–ceramic serves as a key material for ultraprecision imaging of lithography lens, and low-deformation machining is of significance for achieving high-quality surface. Aiming at controllable processing, the annealing of different nanoscratches on glass–ceramic was investigated for revealing the mechanism of material removal and damage repair. The volume change of the single-pass nanoscratch under various normal loads and sliding velocities before and after the annealing was calculated for quantifying the contribution of shear flow, densification, and residual stress to the material removal, respectively. It is found that ductile removal under high normal load or low sliding velocity is dominated by shear flow, thereby improving removal efficiency and reducing machining deformation and defects caused by densification and residual stress. The changes of microstructures beneath the scratches before and after annealing further reveal that the excess processing energy will be absorbed in glass–crystal interface and form micro-cracks on crystal surface. For comparison, brittle removal under variable cycles was simulated by multi-pass nanoscratches, and it reveals that the shear flow ratio raises gradually with the increase of cycle number. These findings provide theoretical guidance for ultraprecision processing of glass–ceramic surfaces.