Sound joint of hollow-extruded 6005A-T6 aluminum alloy was achieved by friction stir welding and its high cycle fatigue performance was mainly investigated. As a result, the joint fatigue limit reaches 128.1 MPa which is 55% of the joint tensile strength. The fatigue fracture mainly occurs at the boundary between the stir zone and thermo-mechanically affected zone due to the large difference in the grain size. This difference is caused by the layered microstructure of the base material. The shell pattern with parallel arcs is the typical morphology in the fracture surface and the distance between arcs is increased with the increase of stress level. The specimen with the fracture located in the stir zone possesses a relatively low fatigue life.