The size of friction stir welding joint has a very important influence on its mechanical properties, welding speed and stability of welding process. The microstructure and properties of friction stir welded joints of 3.5 mm aluminum alloy for rail transit under different tolerance states were studied. The weld performances under the condition that the tolerance deviated greatly from the standard value were compared. The results show that when the upper and lower overlap gap of the joint is greater than 0.4 mm, the weld is easy to appear welding defects, and the welding process window is narrow; when the rotate speed is 1 600 r/min and welding speed is 1 200 mm/min, the weld performance decreases significantly with the increase of welding gap.