Micro-hole structures are widely used in aircraft engines, but they are difficult to fabricate because of stringent machining quality requirements. Electrochemical discharge drilling (ECDD) is a hybrid machining method for fabricating small holes in nickel-based superalloys that uses low-conductivity salt solution as the working fluid. Electrical discharge and electrochemical dissolution occur simultaneously in the ECDD process. ECDD is expected to achieve micro-holes with high machining efficiency and without any recast layer, but little research has been carried out on the surface integrity. In this study, the surface morphology, element composition, residual stress, microhardness, and recast layer properties of the ECDD machined holes were analysed. The results show that the surface integrity of the holes improves by the ECDD method, and there is no recast layer, no melted debris, and no tensile residual stress. Moreover, with an increase of the working fluid conductivity from 0.005 to 3.6 mS/cm, the residual stress of the ECDD machined hole becomes compressive, the microhardness of the wall no longer decreases significantly, and the surface roughness of the wall decreases to Ra = 1.69 μm. Furthermore, the average diameter and the taper angle of ECDD machined hole increase with the increase of machining time. In addition, the entrance of the ECDD machined hole has a round corner without a sharp edge, and its radius-of-curvature is approximately 150 μm.