The invention belongs to the field of hole machining, and particularly relates to a coupling hole precision machining method. The method includes clamping a workpiece on a rotary workbench of a five-coordinate numerical-control drilling machine, machining a first hole of coupling holes in a numerical-control manner, detecting the actual internal contour of the first hole in a layered manner through a contact probe, calculating the actual axis of the first hole by the least square method, reversely calculating the drilling point coordinate of a second hole according to the design parameter requirements of colliding points, regenerating the numerical-control machining program of the second hole, and machining the second hole automatically. According to the method, on the basis of an integral strategy of measurement and processing, contour measurement, data processing and hole machining of the coupling holes can be completed by clamping the workpiece once, the machining requirements for colliding precision of coupling holes with different diameters and inclined angles can be met, machining efficiency is high, precision consistence is high, 'zeroing' processing of machining errors is performed on the colliding points, and coupling hole precision machining is realized.