Nickel-based superalloys are widely used in key micro-hole components of aero-engines due to their excellent high-temperature chemical and mechanical properties. This work focused on tool wear and surface integrity during micro-drilling K4169 nickel-based superalloy utilizing developed new PCBN double-point-angle micro-drill (PDPA-MD) with a diameter of 0.4 mm. The evolution of tool wear characteristics and wear mechanism of PCBN micro-drill are analyzed, and the micro-hole surface integrity is systematically evaluated from the aspects of hole entrance morphology, hole-wall roundness, microhardness and microstructure of subsurface deformation layer. The results show that, the tool wear zone of PCBN micro-drill is concentrated in the chisel edge and the flank area close to the main cutting edge, and the tool wear mechanisms mainly include adhesive wear, abrasive wear, and micro chipping. Distorted grains with plastic slip bands are observed in the plastic deformation layer around the hole entrance of the processed superalloy micro-holes. The closer the grains are to the hole-wall, the denser the distribution of slip lines inside the grains, and the higher the microhardness value of the subsurface layer material. Compared with ordinary PCBN micro-drill, PDPA-MD has better wear resistance, the micro-holes processed by PDPA-MD have smaller roundness error and hole-wall roughness, lower microhardness of the subsurface plastic deformation layer, which significantly improves the surface integrity of the superalloy micro-hole.