The invention discloses a method for machining spatial holes by using a large ellipsoid on a numerical control boring-milling machine. The method comprises the following steps of: determining the range and the clamping datum of a machined hole by applying a software analysis workpiece; compiling a numerical control machining program of the spatial hole; checking the numerical control machining program by applying simulation software; clamping and correcting according to a numerical control requirement and machining the spatial hole with an allowance; detecting the spatial position precision of the machined hole, adjusting the numerical control machining program according to a detection result and then machining the spatial hole to a required precision; and repeatedly clamping and machining a spatial hole in another range until holes on the workpiece are all machined. The invention has the advantages that multiple groups of spatial holes on the large ellipsoid can be machined by using a numerical control boring-milling machine, thereby meeting the requirement on the position precision; the maximum utilization ratio of a process is realized without being limited by the system of thenumerical control boring-milling machine, and the compiling of the machining program can be finished only by updating part models and mathematical parameters; and the process is safe and reliable andhas high efficiency.