Aerospace products have large structural sizes, complex surface shapes, and high assembly accuracy requirements. As automated assembly equipment, mobile robots can achieve precise positioning of aircraft surface crawling and moving assembly poses as well as compensate the relative positioning error between the tool center point of the hole-making robot and the workpiece. Aiming at the requirement of the three-dimensional recognition and measurement positioning of assembly datum under the core clip interference, we propose a high-precision positioning method for the hole-making datum of the orbital crawling robot. First, the adaptive contour extraction algorithm based on gray-scale clustering is used to achieve the segmentation, recognition, and coordinate calculation of the reference hole contour. Then, the three-dimensional conversion of the reference hole coordinates is realized using the target-type high-precision hand-eye calibration method. Finally, a visual measurement system is integrated on the hole-making equipment, and field testing and accuracy verification are carried out. Experimental results show that the positioning error of the reference hole of the method is less than 0.05 mm, thus meeting the assembly and positioning requirements of the orbital crawling hole-making robot.