The invention discloses an industrial robot cutting processing system and a method applied to aircraft auxiliary assembly, comprising a six-axis joint typed industrial robot, a robot controller, an operation panel, a high speed electric mainshaft, a tool clamping process device, a tool quick exchanger, a target installation flange and a laser tracker; high speed cutting technique is adopted; process methods and hole preparing process of boring, reaming by milling and final reaming are sequentially carried out so as to improve the diameter precision of the hole; meanwhile, the cutting force can be controlled by finishing the reaming hole; rough milling is carried out firstly, fine milling is subsequently carried out; furthermore, the cutting depth is not more than 0.15mm during the fine milling process, thus ensuring the planeness of the processing surface; the industrial robot cutting processing system can realize various cutting processes of the soft metal (such as aluminium alloy) as follows: boring, hole enlarging, reaming, dimpling, surface milling, cutting, etc. The invention integrates normal robot, high speed electric mainshaft, quick exchanger, etc., and can solve the cutting process problems of operations such as fine processing, skin cutting, and the like of radar cover installation hole in the field of aircraft assembly.