The invention discloses a large-scale thin-wall skin self-adapting equal wall-thickness milling system and a processing method thereof. The large-scale thin-wall skin self-adapting equal wall-thickness milling system comprises a contact probe, a contact probe signal receiver, a five-axes numerical control machine tool, a PC machine, a path measuring planner, a path measuring emulator, a curved surface reconstruction device, a thickness distribution fitter, a thickness compensation cutter track planner, a cutter track emulator and a supersonic wave thickness meter. In the invention, the surface morphology and thickness of a large-scale thin wall member can be respectively obtained through the contact probe and the supersonic wave thickness meter, an actual contour curved surface can be reconstructed by using a curved surface reconstruction device, then an actual thickness of the curved surface is calculated by using the thickness distribution fitter, the actual thickness and a theory thickness are compared through the thickness compensation planner, and then the thickness compensation cutter track can be obtained, so that purposes of higher automation degree and better processing precision can be reached.