Abstract: Friction stir welding (FSW), as an advanced solid-state joining technique, has been widely applied in the welding of aluminum alloys. However, owing to factors such as the tool structure and the inherent properties of the materials, the joints are prone to root kissing bond (KB) defects. This kind of defects not only severely impairs the mechanical properties of the joints but is also difficult to detect using non-destructive testing methods. To address this issue, this study explores a novel process—vortex flow-based friction stir welding (VFSW)—to eliminate KB defects formed during the FSW of aluminum alloys. Comparative experiments between VFSW and FSW were conducted to investigate the mechanism by which VFSW eliminates KB defects. On this basis, process validation of the VFSW process were carried out on 2219 aluminum alloy to identify the appropriate process parameter window. The joint quality was then evaluated through microstructural analysis and mechanical properties testing. The results show that the plastic material vortex formed at the bottom of the stir pin during VFSW can drive the material flowing sufficiently at the root of the weld, effectively eliminating KB defects. Under optimized process parameters, sound welds free of KB defects were achieved. The tensile strength of the joints increased with welding speed, reaching up to 330 MPa, and fracture did not occur in the regions prone to KB defects. These findings confirm the feasibility of VFSW in eliminating KB defects, providing an effective approach for achieving high-quality joints in aluminum alloy FSW and laying a theoretical foundation for its engineering application.