In this paper, the microstructure of friction stir welded between the Al–Li–Cu alloy and the Al–Zn–Mg–Cu alloy was studied using optical microscope(OM), electronic backscattered diffraction (EBSD), SEM, and TEM. The hardness profile revealed that the range of heat affect zone for the Al–Zn–Mg–Cu alloy was slightly wider than the Al–Li–Cu alloy when they suffered from the thermal transient. Additionally, the characterization of precipitates inside the different zones was obviously different, which corresponded to the microhardness distribution profile. At the periphery of the kissing line, the Al–Li–Cu and the Al–Zn–Mg–Cu alloys mutually diffused during the weld process. The magnesium element in the Al–Zn–Mg–Cu alloy diffused into the Al–Li–Cu alloy. But the copper and zinc had no change because of the low diffusion coefficient in aluminum. The heat affected zone of the Al–Zn–Mg–Cu alloy showed a higher corrosion susceptibility immersed into the corrosion environment, and the Al–Li–Cu alloy did not show severe corrosion.