In this paper, the microstructure in the nugget zone of a friction-stir-processed Al-Cu-Mg alloy was analysed. There are the irregular bulk precipitates and micro-voids in the Al-Cu-Mg alloys. These precipitates were the compounds of Al-Cu system, and the size is less than 1 µm. In a local area, the homogeneous amorphous structure of Al-Cu system in some area of the nugget zone was also detected. The amorphous structure with a halo pattern has a structure characteristic of the long-range disorder. The formation of micro-nano and amorphous structure in the nugget zone could be attributed to the severe plastic deformation, breaking effect of stir tool, higher temperature gradient, hydrostatic pressure and shear stress and strain.