Vortex-friction stir welding (VFSW) utilizes a stir bar made of an identical material to the workpiece to rub the workpiece’s top surface, which avoids the keyhole defect in conventional friction stir welding. It presents great potential in the repair field of aluminum alloys. In this study, the effect of stir bar diameter, rotation speed, and welding speed on the weld formation was investigated in the VFSW of 6061-T6 aluminum alloy. The weld macrostructure, penetration, and mechanical properties were characterized. The results show that a large diameter of the stir bar can enhance the vortex material flow, increase the heat input, and eliminate the incomplete-penetration defect. The increase in rotation speed within limits can enhance the weld penetration and the mechanical properties of the weld nugget zone (WNZ). However, too high a rotation speed reduces the weld penetration and weakens the mechanical properties of the WNZ. The increase in welding speed reduces the weld penetration but enhances the mechanical properties of the heat affected zone. The incomplete-penetration defect significantly weakens the ductility of the VFSW joint. It can be eliminated by enlarging the stir bar diameter and choosing a moderate rotation speed and a lower welding speed.