Nickel-based single-crystal superalloy has no grain boundary. This makes the traditional cutting mechanism of shearing and slipping along grain boundary of polycrystalline material based on the theory of elastic-plastic deformation not suitable for drilling single-crystal parts. To achieve high-quality and low-damage micro-drilling of nickel-based single-crystal superalloy, the micro-drilling surface/subsurface quality of the (001) crystal plane of nickel-based single-crystal superalloy was studied in this paper. Firstly, the influence rules of the cutting speed (v s) and the feed rate (v w) on the micro-drilling hole size, surface morphology, surface roughness and subsurface damage depth were studied. Then, the micro-hardness on micro-drilling subsurface was analyzed. Finally, the subsurface recrystallization was explored. The results show that with the increase in v s , the hole diameter error and the surface roughness decrease, and the depth of subsurface plastic deformation layer decreases first and then increases; with the increase in v w , the error of hole diameter and the surface roughness increase, and the depth of the deformation layer decreases first and then increases. When v w > 0.33 μm/r, there are severe scratches on the surface of the hole wall, and the hole wall appears undulating stripes; white layer structure and severe plastic deformation layer appeared on the micro-drilling subsurface; the γ and γ' phases' deformation is severe; the micro-hardness at the subsurface white layer is small, and the micro-hardness value at the plastic deformation zone is large; after the hightemperature treatment, γ phase dissolves on the subsurface of micro-drilling parts, and the cellular recrystallization and the complete recrystallization occur. The minimum thickness of recrystallization layer obtained is 1.43 μm at v s = 141 m/min and v w = 0.105 μm/r. This study provides a good guidance and reference for the machining of nickel-based single-crystal superalloy micro-hole parts.