The effect of pre-welding cleaning on the S-line and properties of the FSW joints of the aluminum alloy thick plates was studied by contrast of the specimens with pre-welding cleaning and without pre-welding cleaning. The following conclusions were drawn from a series of experiments. The pre-welding cleaning helped to improve joint microstructure. At the same time,the effect of pre-weld cleaning on the FSW joint was shown to weaken the S-line,especially the width of the S-line. The pre-weld cleaning could also improve the mechanical properties of joints.