The invention discloses a multi-mission aircraft auxiliary assembly system on the basis of an industrial robot, comprising crossing movable platforms which are symmetrically arranged at two sides of an aircraft shaft movable platform, an industrial robot, a tool garbage, a traveling lifting operation platform and a compacting mechanism, and a target installation flange and a took quick replacing device which are arranged at the end flange of the robot. The crossing movable platform comprises an upper layer of platforms and a lower layer of platforms and can move along the flight course and the wing extension direction of the aircraft; the movable industrial robot faces to the aircraft shaft when at the zero position; the tool garbage is arranged at the rear side of the robot; the operation tools hang inside the tool garbage according to codes and the automatic replacement of the tools is realized by the tool quick replacing device; the operation flow control and state monitoring of the whole system are carried out by a robot operation platform; the multi-mission aircraft auxiliary assembly system can be applied to the aircraft automation, flexible assembly production line, and completes the auxiliary assembly operation missions such as taking and positioning of system part, bore preparing of part butting surface, plane milling, punching of measuring points, etc.