Manufacturing accuracy, especially position accuracy of fastener holes, directly affects service life and security of aircraft. The traditional modification has poor robustness, while the modification based on laser tracker costs too much. To improve the relative position accuracy of aircraft assembly drilling, and ensure the hole-edge distance requirement, a method was presented to modify the coordinates of drilling holes. Based on online inspecting two positions of pre-assembly holes and their theoretical coordinates, the spatial coordinate transformation matrix of modification could be calculated. Thus the straight drilling holes could be modified. The method improves relative position accuracy of drilling on simple structure effectively. And it reduces the requirement of absolute position accuracy and the cost of position modification. And the process technician also can use this method to decide the position accuracy of different pre-assembly holes based on the accuracy requirement of assembly holes.