Single crystal YAG is extensively employed in the manufacture of high-power lasers due to its stable physicochemical properties and excellent optical performance. However, there are few studies on the mechanisms of material deformation and removal, and a lack of research on the interactions between abrasives hinders the advancement of ultra-precision machining for this crystal. During this study, single crystal YAG was subjected to the varied-load single nanoscratch test and constant-load double nanoscratch tests using a nanoindenter. The main characterization methods include scanning electron microscopy and transmission electron microscopy. The microscopic characteristics of the material surface and subsurface following scratching were systematically examined, and the effects of abrasives interference on deformation and material removal mechanism were studied. The findings show that slip bands and cracks occur primarily along (001) crystal planes and (110) crystal planes. Bifurcation, deflection, and discontinuity occur during the expansion of the cracks. Amorphous and nanocrystals were also observed in the crystal subsurface, accompanying the formation of atomic-scale defects, such as dislocations, wrong arrangement of atomic planes, and lattice distortions. In comparison to the single nanoscratch, the double nanoscratch is more susceptible to crack formation on the crystal surface. The interaction between the scratches causes the second scratch to be deeper than the first scratch, facilitating the occurrence of transverse cracks under low loads and increasing the number of median cracks. The findings enhance the comprehension of the deformation characteristics of single crystal YAG and hold significant implications for damage control during its ultra-precision machining.