In this study, a modified stir tool with a disk at the top of the probe was used for friction stir welding (FSW) of 6061-T6 aluminum alloy. The effect of the disk at the top of the probe on the thermal history, microstructure and mechanical properties of the resulting FSW joints was investigated. The results showed that the disk could increase the peak temperature, prolong the thermal cycle and improve the material flow at the welded bottom. As a result, root defects were eliminated and the microstructure of weld bottom was homogenized and refined due to more sufficient dynamic recrystallization. The tensile strength of FSW joint produced using the probe with a top disk was about 243 MPa, reaching 77.9% of the BM, while that of FSW joint produced by the probe without a top disk was only 204 MPa, as much as 65.4% of the BM acquired. The FSW joint produced by the modified tool exhibited ductile fracture with the cracks initiated and propagated from the softening zone, while a mixed-mode of ductile and brittle fractures occurred in the FSW joint produced by conventional tool, which originated from root defects at the bottom of the weld.